Most likely he will just cut out a piece for the biopsy. The reason being is that if it is cancer, heaven forbid, you will need to have a doctor cut it out so they know that they got it as well as the margins around it. If your oral surgeon cuts it out, the doctor won't know where the margins are to make sure there was not any local spread. At that point they will then test the margins to see if there was spread and develop a treatment plan from there.
It probably is nothing, but please make sure to follow-up with a biopsy if it doesn't go away-regardless if you have pain or not.