Well, she killed loads of people, even though it was an accident, so why shouldn't she have been in prison? If they knew Crossbones was going to be there they could have tipped off the military and picked up their vans outside of town - it was the Avengers that chose (with no authority in that country) to engage them in a VERY public area surrounded by people. They weren't even "supervillains", just mercenaries that Cap had beef with, and he's running operations on foreign soil to stop them, with no permission or authority there.
I've been in two minds, but I'm leaning to Team Iron-Man.
By the end, Iron-Man is Ross' little ****** on speed-dial, and anyone who was against them is in prison, so Cap was right about that and Iron-man knows it.
BUT
With Zemos motivations clear at the end... EVERYTHING was about Sokovia. Every action, every death, the death of T'Chakka, it was all just fallout from Sokovia. Not a thing happens in this entire movie that isn't indirectly caused by the Avengers and/or their irresponsibility and failures in AOU.