In the book Wiseguy (which is the book that Goodfellas is based on) it says that after Henry went to prison Tommy DeSimone (Danny Devito's character is based on) that he tried to have sex with Karen and when she refused he tried to rape her. Apparently Tommy getting whacked under orders by Paul Vario (Paul Cicero- the Lucchese Capo in the film) was partly in revenge for DeSimone's attempted rape (it was another excuse to put Tommy down because he was out of control).
None of this was included into Goodfellas, however it gives you an idea of what Jimmy's fate may have been if he had killed Karen; clearly Vario was against women being involved in violence, etc.
So i doubt that Jimmy really would have whacked Karen...