I only watched the first couple seasons of The Boys (somehow less edgy than the comic book!)

But Huey slowly coming to the realization that sometimes the enemy can't be defeated through the system and sometimes there are controlled opposition on "your side" working to just hinder your movement and you really do gotta come out and kill people sometimes.

Now it's not him siding with the villains, so much as a liberal realizing the futility of non-violence and working within the system, and joining up with a guerilla terrorist group that eventually gets recruited by the CIA is surprisingly realistic for a superhero show made by Amazon.

I think that happens in every ghost in the shell arc.

Not a movie and I haven't finished it, but I believe The Rose of Versailles does this. The main character is a royal guard for Marie Antoinette who starts out only seeing the perspective of the nobility, but gradually sees more and more of the horrific conditions regular people are dealing with on a regular basis and joins the revolution.

I hate to say it cause it is so mediocre but, Captain Marvel is exactly this idea

Is Ex Machina a good example? I mean the 'hero' ends up not on the 'villain's side at the end but for reasons that have to do with the villain being too right for the hero.

That's just an antihero

There's a mecha movie with a surprisingly fun plot twist at the very end called Robot Jox. Both the villain and the hero are being screwed by their government sponsors, and ultimately...

EDIT: I said "bad" but actually I enjoyed it.

Crouching Tiger Hidden Dragon and Joint Security Area both feature something kinda like this, but the "villain" is presented sympathetically from the start, and both sides develop instead of just having the antagonist change for the sake of the protagonist. Decision to Leave might be closer, but I get the feeling you're looking for a movie that might involve political conflict and that movie is focused on few interpersonal conflicts.

Suzaku's arc in Geass is kinda like this. Of course it's all insane but there's definitely an element of what you're talking about.

Not a movie, but the first three books Glen Cook's The Black Company are basically this arc.

The Watchmen. I'm thinking the books, but I guess there's a movie too.

Hero (2002), a Chinese movie about a guy who realizes that peasants are scum and need the iron fist of a just and kind ruler to keep them civilized. He initially planned on murdering the benevolent monarch because peasants are nothing more than barbaric, uneducated fools, but he shows that rare trait after so long of finally realizing that obviously a monarch would know better, and they basically work together to fight the system, but the monarch is forced, reluctantly and painfully, to give the idiot peasants what they want and have the guy executed.