Hell, Tony probably came to him willingly because Tony trusts Steve so damn much. And Tony didn't know what Steve was really planning and he they could talk about this -- and he figure maybe something was controlling Steve.

With Stephen Strange who knows -- though in my head he and Pepper are together in his universe (and lets face it a great many in my head), so maybe she was able to get word to him via Tony to go into hiding. Which might explain how she kept from being killed or captured, if she was in hiding with him.

Nah, no skrulls in this. And Spider-Woman is dead dead dead.