We don’t see Abigail kill anyone first hand and we certainly aren’t made aware of her doing so (with the exception of Mr Milton himself - funny that in later years John chooses to go by that name). So to our best knowledge up to that point she hasn’t actually killed anyone. Certainly when she kills Milton it seems like it’s her first kill.
Thing is as said above she’s associated with a group of murderers and this is well known to the Pinkerton’s because they interact with her in a hostile manner when Hosea is captured. She was also witnessed by both Ross and Milton at the gang’s camp in Clemens Point. So Abigail is certainly an accessory to murder and can be charged and convicted of such. Of course Milton is ruthless and unafraid to twist the boundaries of the law in order to get what he wants. He could very easily fabricate a murder charge for Abigail that was linked to the bank robbery in Saint Denis since she was witnessed as being involved. Considering how violent the bothched robbery was ultimately, he could very easily draw a correlation between the number of casualties and Abigail’s presence to charge her with murder.
The evidence would indeed be circumstantial however it could not easily be proven that Abigail didn’t kill someone during the robbery and Milton would argue her presence at the scene as well as her history of fratinisation with known killers would be enough to fulfil her mental willingness to commit such a crime; he would also use her escape from capture against her playing it up as violent, he would find out which deceased lawmen personally interacted with her during those events and use that as an excuse to frame her for murder. He would be able to provide witnesses that could confirm there was interaction to support his claim.
Furthermore, considering his position he could bribe or threaten his underlings to provide false testimony against Abigail which, wouldn’t be questioned as Milton publicly would be seen as a capable lawman. I think he knows for a fact that Abigail wasn’t present during Cornwall’s murder as he spoke with the man mere moments before Dutch killed him and most likely heard the gunshots so it’s highly likely he was made aware of the shooters.
The General would be much harder to fabricate as it was a dispute between the rights of the Native people’s of the region and the American army so it would be a stretch to add Abigail to this scene especially considering it is only really Arthur and Charles that take part in many of the hostilities. Dutch does also but the only major assistance provided by the Van Der Linde gang is at the Cornwall Kerosene Oil and Tar Company drill site which Abigail is not a part of.
It’s easier to frame Abigail when he has witnesses present, so Saint Denis seems the best choice for Milton to fabricate charges. However his reasons for doing so are quite obviously simply to lure out the Van Der Linde gang. He by now knows John’s value in the gang (he perhaps would only be partly aware of the true situation from Micah) so he knows that if he captures Abigail then John’s gonna come for her and he also knows if John comes then Arthur will probably join him and so to then would Dutch or at least he hopes that will happen.
Although we know Micah’s ratting we don’t know to what extent he told Milton the full truth. Micah is an opportunist and seems to be convincing Dutch to engage in his more violent side for fun but then also enjoying the trust Dutch begins placing in him. I think it’s highly likely Micah is actually playing both sides. I think Micah would have told Milton that there was a little tension between John and Dutch to show that Milton’s work was paying off in causing the gang to fracture but he probably also said if you take Abigail then John will come after her, Arthur will come for John and Dutch will come for Arthur. So to Milton who would be feeling pressurised following the death of Cornwall since he had not only failed to bring Dutch to justice but allowed him to walk into town and murder Milton’s own benefactor would be attracting serious attention from his competitors both within the Pinkerton’s themselves and outside in other legal institutions and the public.
Milton when he took Abigail was desperate because he had failed. He threatens Abigail because he has to bring someone in but he hopes she’ll act simply as bait for a bigger fish. If she fails to lure John or Arthur in then he can play up her role in the Saint Denis bank robbery to make himself appear competent. He knows by capturing a member of Arthur’s stature within the gang he would receive a massive boost to his public image and most likely his funding as well; if he brings in Abigail on false charges and successfully gets a conviction, he can at least save face publicly and buy himself more time.
It would also, perhaps unknown to Milton, further drive a wedge between John and Dutch as Dutch simply wouldn’t care about Abigail being captured or convicted as he blames her for poisoning John’s mind against him. This in turn helps out Micah who would then provide further aid to Milton by pouring salt on the wound between John and Dutch to cause further friction in an attempt to drive away both John and Arthur whom Milton could them simply pick up in a manner similar to how Strauss was captured. Without a doubt John and Arthur would go after Abigail and likely have assistance from Sadie which Micah could then use to aid Milton in capturing them.
In capturing Abigail, Milton’s banking on Micah’s word being right, which it is, whilst Micah is hoping to remove both Arthur and John from the competition. Since John is gone, presumed captured or killed, it falls on Arthur. Milton sees an opportunity and captures Abigail. Arthur comes to save her and Milton ends up getting killed by Abigail when he attempts to murder Arthur himself perhaps both out of desperation for a result and simple hatred of Arthur for the trouble the gang has put him through in pursuit of Dutch.
Milton fails totally and Arthur and John both return to plague Micah, the latter eventually killing him. Ross assumes control of the Pinkerton’s and proves he is a far better leader than Milton by assaulting the gang’s hideout which both completely splits the gang (at least in the public’s view) and results in the death of Arthur Morgan, Dutch’s right hand man.
In one decisive move, Ross usurps his predecessor’s effectiveness in the public’s opinion, cementing his position as the person to eventually be put in charge of the Bureau of Investigation several years later simply by ordering a full scale assault on the gang’s hideout and seeing both Arthur killed and the gang totally destroyed. Dutch goes his separate way abandoning the rest of the gang, Micah also goes his own way, likely with Cleet and Joe and forms his own gang and it’s very possible Javier and Bill go off on their own with Javier eventually deciding to head back to Mexico and Bill deciding to form his own gang in New Austin.
Milton was desperate for a win at that point, his consistent failure to have any real measure of success was draining him. Cornwall was threatening to remove funding because he was failing to see enough results. Then Cornwall was murdered and Milton was in the town when it happened. Not only would Cornwall’s money cease, his reputation is severely damaged.
He could easily fabricate murder charges to threaten Abigail in the hope that it might draw another gang member in, which it does, because he now, more than ever, has to present a result that proves his capability in bringing in Van Der Linde himself. Milton has lost financial support and had his reputation tarnished publicly by Cornwall’s murder. To gain any of it back he has no choice but to deliver so he grasps at whatever he can get. The opportunity he gets is capturing Abigail and he once again fails.
