Scarlett recently talked about working with her stunt double, Heidi Moneymaker, who has done all of the Marvel films with her. Heidi is the one who came up with that unique take-down move from TA. I'm sure this just means that Heidi will handle all of the stunts for AOU, though there are probably some things that Scarlett can do. The film is already scripted so it should be easy for Whedon to work things out so that most of Scarlett's scenes are filmed immediately, to account for her pregnancy. There shouldn't be a problem at all, as she is likely very early on.
It's really despicable when people in Hollywood penalize actresses for becoming pregnant. Not only are there laws covering this sort of situation, there is also common decency to consider.