Does anyone else have trouble with the aspect of the plot where Marston supports and helps both Allende's forces and the rebels? In terms of Johns morality and the story itself, it doesn't seem to make a ton of sense to me

So I'm replaying RDR again, and I am currently in Mexico, nearing the end of my time at this point in the plot. Just killed De Santa and I've been thinking a lot about this part of the plot and having some difficulties with it.

Here is my issue...

(1.) John says he's done with his criminal past. He's this weird, enigmatic, paradoxical sort of character who seems to say and do a lot of good things while also saying and doing a lot of bad things (past and present). But ultimately, he suggests he's put his rough past behind him and indicates that he's better than Williamson and Escuella for having done so. But supporting a tyrannical government who kills citizens at whim, rapes women, and massacres entire towns doesn't seem to be putting the past behind. In fact, that seems even worse than he's gang-related past-- I'd consider robbing banks less evil than being accessory to the massacring and burning of towns. You can see his disdain for the actions of Allende and De Santa, but he still helps, and I say that makes him just as guilty. I know John says his family comes first and this is all for his family, but he's also aiding in the massacre and rape of tons of people who also have wives and children. Can anyone reconcile my issues here?

(2.) In terms of the plot, it just doesn't make much sense. John goes and kills a hundred rebels for the government. Then John kills a hundred soldiers for the rebels. You're telling me no one on either side starts objecting? Obviously, De Santa attempts to have John killed eventually, but that's pretty late. Despite John killing a hundred or so rebels and revolutionaries earlier, Reyes has an army of rebels come save Marston from certain death. Seems slightly dubious to me that the rebels would be so willing to embrace him on missions and help him escape death after him having killed a ton of them. Thoughts?