H.F.
If the dentist thinks this is necessary and the periodontist does too, then get it done!!! I do know that infection or decay can get to the bone of your jaw and you do not want that!!! So be comfortable knowing that this is a short-term discomfort to prevent a long-term problem.
Make sure that your doctor knows about your anxiety ahead of time and maybe he can do the procedure with you under general anesthesia (they put you to sleep completely). This would require someone taking you and picking you up and you would have the discomfort of the anesthesia wearing off, but you wouldn't be sitting there fretting about every push, pull and tug during the procedure. If your doctor doesn't seem concerned about it, remember even though you are only going through it once and it is scary to you, these guys do this kind of thing all the time! Good Luck