You're not making any sense. You say the general audience wouldn't be confused, to not use that excuse, then you say the GA aren't as stupid as ppl make them out to be. LOL if they're not so stupid, they should be able to figure out that she was just in MOS playing a villainous character. If they cant figure that out then they should be treated as oblivious people. "Oh look Superman is now teaming up with his enemy!" anyone who has seen MOS at that point should be able to figure that out, cmon.
It doesn't matter what happens to her in MOS, it would be incredibly stupid to put her in a different role, especially one that is so different while standing next to Superman to fight evil. Im sure there's better options out there.
Chris Evans is irrelevant. Fantastic Four and Captain America/Avengers are not in the same universe.