I have to wonder if the Bucky shot with Tony is a flashback moment. If that attempt to kill him is after they take sides / present, it makes it pretty clear which side is in the wrong.
Ideally, I would be on Capt's side. Given the corruption has not been cleared in the governments and we know Hydra was pretty entrenched, seems to make it clear the Avengers teams should be the ones to make the decisions, not a world governing body. That and the ramification of micromanagement by such. Of course, if they follow the comic's past history...
Assuming Thanos also does get the infinity gauntlet, any death can be turned around in the future, so with this film series, they could get as bloody/deadly as they want and have an out in the Avengers Phase 3 showdown.