... Just out of curiosity, was I the only one who felt like rooting for the human side, even though I consciously knew they were the bad guys?
No, Quaritch did nothing wrong.
Hometree was an inside job, tear gas can't melt lignin beams. Legitimately, he did nothing wrong. You can play the happy music every time a human dies, but they were there to dig for minerals the Naavi didn't give a shit about. The humans tried to provide medicine, education, build up cross-cultural links and the Naavi were being giant carbon dicks about everything. So the humans send in the avatars to try and explain why the humans are there. Unfortunately the highly-trained diplomat guy dies and is replaced by the incompetent Jake Sully. The incompetent Jake Sully fails to explain why the humans are there, spending his time boning alien cat princess, and instead of trying to use any of his influence to negotiate between the human factions and naavi factions (HIS ONE FUCKING JOB) he fucks up to fuck his blue waifu.
Cut to the humans who begin building their infrastructure, where they begin clearing a path to the mineral deposit. They destroy a sacred tree. A tree they did not know was sacred, because the people they tasked with understanding the Naavi couldn't be asked to explain to their colleagues that killing tentacle tree is haram. Instead Jake Sully destroys the cameras of the digger, literally doing the opposite of his job by making the humans go even more in the dark. When they finally reach Hometree, after Jake Sully's inept efforts have failed, they first try clearing hometree nonlethally and only move to leveling it after the Naavi try using it as a launchpad to attack the skyships. When Jake finally gets off his arse to do something, he decides the best course of action to dealing with Quaritch is to kill him, so he assembles his great big army. Quaritch, seeing a massive fuckhueg army of blue giants, himself only fielding
merchants, and not even the militant merchants like the space east india company - no we're talking space indian cornershop tier merchants, notes that Jake Sully has assembled 20,000 soldiers where before there were 2,000 and they were continually growing in number to the point where they could reach 200,000. Only then does Quaritch do the only thing that could save the human compound from being entirely overrun: Attack their tree God. Their tree God is especially notable for having assimilated human generals and scientists, giving it dangerous knowledge it could use against the human species.
Thanks to Jake Sully, after the movie ended, the human merchants will have made it home and human
soldiers will have returned. Dropping tungsten rods onto their tree God from space.