I had the bottom ones surgically removed about a year ago, one tooth at a time and about six weeks in between the operations. Same situation, they were barely showing.
The operation was very quick and painless, it was about 20-25 minutes per tooth. They gave me some hefty painkillers to go, but honestly there was no need for any kind of pills as the wound itself wasn't actually hurting at all. The jaw bone was a bit sore for a day or two, but it was only noticeable when I opened my mouth so that wasn't a problem either. I did get a little bit of swelling with the first one, none with the second. They used dissolving stiching, but it took almost three weeks to dissolve so after the second operation I had the stiches removed some ten days later as the most incovenient thing about the whole operation was having those bits of half dissolved threads in my mouth.
So yeah, don't worry about it. It's really not a big deal. I actually disliked the pulling of the upper wisdom teeth more than the surgical removal. Pulling wasn't at all painful either, but I couldn't sleep for a day or two since I kept hearing the sound of ripping that tooth out in my head and getting shivers because of it..