To be honest after Bendis' made her a supporting character in Iron Man's corner it would be more unbelievable than ever if she was uncomfortable. When working with Iron Man and all the crossovers Iron Man was involved with, she dealt with Tony Stark, Doctor Doom, the POTUS, the Guardians of the Galaxy, the Thing, Ironheart and others. She basically dealt as Stark's PA with all kind of earth, global, geopolitical and galatic stuff. Sitting down for dinner with the Lizard Connors' is the least of it.
I always thought Bendis making her a supporting player in Iron Man was part of a long-term gambit on the part of a guy who is I think a Peter/MJ shipper. He made sure there was no relationship, the one scene where MJ and Tony might have something became an exercise for MJ to mock Tony for slumming it, and by making MJ a business executive at the same time Peter became one in Slott's Worldwide he made sure that MJ remained the only person to truly equal Peter.