I thought Whoopi was done with acting.

No, she's still acting. She's actually reprising the role of Dolores Van Cartier in a British production of the stage musical version of "Sister Act", in addition to other roles she takes on.

EDIT: As to the possibility of a Sister Act 3, Disney has been revisiting a lot of their old properties, so such a film wouldn't surprise me if it went through.

I kinda hope it happens.