Are you missing any of your 1st or 2nd molars? It is not standard practice to use 3rd molars in anchoring for orthodontics, unless there are no other molars. 3rd molars are a major PITA to restore due to access. The human anatomy does not allow most people to open their mouth enough to get a drill back there along with everything else needed to restore the tooth. I do not envy your dentist, but applaud him/her for being so eager

My personal standard of care is to typically use minimally invasive restorations, especially on a 3rd molar. If the tooth is badly broken down then you obviously cannot keep it clean. What is the perio health like back there? It is possible that if you cannot keep your 3rd molars clean you can put the teeth adjacent to them at risk as well. Are they even in occlusion? My experience is that most people with decayed 3rd molars will have recurrent problems even with a restoration. I would explore having them extracted before your treatment, unless your ortho has treatment planned a use for them.
Good Luck,
Rory