I had a cyst removed that was large enough that it had damaged my right ovary & fallopian tube, so they also removed those, but recovery was not bad. (It seems like your wife's cyst isn't large enough that it would necessarily have damaged anything, though.) Laparascopic surgeries are even outpatient-type deals! Her GYN will be able to tell you what you should do, so look for a good GYN if you don't have one already.
I doubt she'd have to get an ovary removed, but even if she does, don't worry about fertility. The left one will take right over. :)
No she will be okay. They may go in and remove the cyst. It's not a bad procedure.I had one done. What does hurt bad is if it burst on it's own.