Isis was a really rare name before ISIS came along. There will always be new terrorists to become the new bad guys, and I'm sure eventually people will not think of the ISIS group when they hear
Isis, because they will be busy caring about someone else. I'm not sure how long that will take, maybe not in our lifetimes, but
Isis (the goddess) has been around a long time. One day
Isis will regain her status as an extremely rare name, I have no doubt. They could always use
Iset in the meantime.