It seems to me, at the end of it all, Tony has cooled a bit since the almost fatal fight. He tried to kill Bucky and brutally beat Steve.
Now he's had some time to think and a bit more perspective on it, as well as not being fueled by emotion.
He's still disagrees with Steve on the Accords. He's still probably angry that Bucky killed his parents and Steve protected him not just from death but incarceration. The whole situation is screwed.
But then again, everyone in that prison is a good person and a hero. Tony knows that. He didn't know they'd be put in the raft and doesn't agree with Ross keeping there without a trial or anything. He didn't want it for Wanda, he didn't like Clint being kept from his family, Falcon is another soldier and loyal to Steve and his friends. They are good people who've saved the World.
So when he gets a call from Ross, and puts it together that they are escaping. He lets it happen. Cause while they are on opposite sides, the alternative is horrible and the World will probably need them again. So having them free and underground at least gives them another chance instead of locked up indefinetly.