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I've seen the film twice and I don't recall either time where Tony made a rape joke. If we're talking about the one-liner that CMIII mentioned, I just thought of it as a crude reference to Nat and Bruce's relationship. No implications of coercion or force.

As for the Romanoffs, blind anger and thoughts of revenge can cloud anyone's mind. Even to the point that logic is no longer a factor. I find it entirely believable that Piotr and Wanda wanted to get revenge on Tony and the Avengers so badly, they didn't care what they had to go through or who they had to work with to accomplish that goal. They also probably didn't care about anyone else by that point (civilians, Hydra personnel, etc).