OMG i can't believe you would put hand sanitizer inside her, hand sanitizer kills bacteria, and women have bacteria that is NECESSARY in the vagina. At the very least she will have a really bad bacterial unbalance, she could get an infection so easily now, like a yeast infection.

Don't ever do anything like this again, and to answer your question, no, it will not kill the sperm!, and even if it did, that's not the way spermicide works!! the semen is already on the way by the time you applied this to her. Oh God!!

If you're worried about this so much, get the day after pill and PLEASE, if you can't afford condoms or any other kind of birth control, and don't want kids... DON'T HAVE SEX!!!