Actually, arguably, it depends on the definition of "innocent"; in terms of the things the Koopa Troop has committed, they aren't innocent whatsoever, and have done multiple terrible things, but in actuality according to Kammy Koopa in the original Paper Mario 64, the Koopa Troop actually has (or had) a noble cause, as she says so herself that the motive of the Koopa Troop is to "have revenge against all who have treated Koopa Troopas poorly", and while it's possible she may have been lying, it would at least explain why the Koopa Troop was so militant even before Bowser fully took the throne.
However this motive has mostly been ignored, likely because most of the Koopa Troop's operations are solely based upon Bowser's interests, so while I wouldn't call the Koopa Troop innocent, I wouldn't necessarily call them guilty either; more or less misguided under Bowser's control.
Still though, I doubt the lowly Koopa Troopas are wringing their hands and plotting their next evil scheme, rather I'm pretty sure that they've simply been manipulated by Bowser, especially because as far as I can tell, only the higher-ups actually acknowledge that what they're doing is evil, while the enemies you fight in normal levels don't really seem to exhibit this.
But hey, that's all speculation, since the enemies typically never talk. From my perspective, as noted before, I don't see the Koopa Troop as innocent or guilty, just misguided. If anything, I think Bowser is the most guilty out of all of them.
And even then, Bowser isn't truly heartless as proven by how he treats Jr., and while I'm pretty sure that Bowser's desire for Peach isn't solely because of love, the fact that it was confirmed in his diary, also in the original Paper Mario for the N64, that he had a crush on her and wanted to steal her from Mario, likely plays a part in some form.
Although given Paper Jam, all of this could just be limited to the Paper Mario series, so who knows for sure.