The best surgical treatment of an abscess/cyst, if there is enough room to repair the skin afterwards, is to remove the entire thing, including the capsule of skin around the pus/contents. The skin can then be stitched up over top. One of my pigs had this done with an abscess on her back and it was a very easy procedure and recovery. The other method of treating an abscess is to lance and drain it- opening of the capsule, squeezing out the contents, and then leaving it open to continue to drain, along with an antibiotic. This will require more aftercare, as the wound is left open and you will have to continue to irrigate the area and express any pus while it heals. Make sure you know going in what process the vet is using and why. It's also good to know that the vet has experience with anesthesia for small animals, etc. It's always best to go with a vet with as much experience with guinea pigs as possible, though I realize that it's not always possible to get to a small animal or exotics or specialty vet. Inhaled anesthesia is safest for the little guys, so you may want to ask about that too.
As for your pigs being okay together again post surgery, personally I've never had a problem taking a pig out for a procedure and then having them not be accepted upon their return (their companions were actually always really glad to see them!) But I have sows, so hopefully someone with boars can weigh in as well.