I feel this is very much a "tread lightly" type of question, but I'd say authentic for the time (as you said, in a respectful way), although I do think you should be able to fight Native Americans in free-roam, as you can with any other NPC.

I say considering Dutch"s Gang in RDR served as a faction of primary native Americans and Americans with native heritage served as the main antagonist group in West Elizabeth. Later in RDR2 the Skinner Brother's were a mixture group of wild frontiermen & native Americans who attack settlers throughout Tall Trees/Big Valley. So with those 2 examples it is possible but must be done in a certain fashion considering audiences who are woke may not like it.

I would've hoped we would've been able to fight alongside the Native Americans, not against them.

^We did in RDR 2 notably the attack on the oil fields

More extensively fighting alongside native Americans Americans would be good

I mean 90% of gunfights and skirmishes in the Old West were between settlers and hostile Native American tribes so it wouldn't be not authentic but they probably won't go for it as it could leave a bad taste in a lotta peoples mouths.

I think if RDR3 were to go further into the past they would definitely have to include it to be historically accurate, but who knows, perhaps if they do that they might actually make a native protagonist experiencing the ‘wild west’ through the eyes of a Native American?