First, fish out the fruit fly.
Then, relax.
Your SCOBY is an ecosystem. It's nothing but symbiotic bacteria and fungi living out their lives. It's not easy for it to become contaminated with a pathogenic microbe. And that's all a fruit fly could do to it. It's already teaming with life -- so it won't pick up harmful things easily. (Just like how your own body is less likely to pick up harmful microbes if your gut ecosystem is working right.)
Give it a few days. Feed it and so forth like always, just don't consume anything it produces. Give it, say, five days. After that time, if there's no visible signs (new colonies of bacteria or fungi growing in an unfamiliar way, off colors) or olfactory signs (i.e. if it smells okay) then you're almost certainly fine.
(This is an educated guess, take it with a grain of salt. I am not your doctor, nutritionist, chiropractor, reflexologist, or faith healer, yadda yadda yadda.)