I don't think you can CNC the holes as fast as a hole saw. A properly made jig will eliminate operator error, unless they are doing it wrong on purpose! If thats the case even CNC won't stop it!
Why not build a gantry type machine large enough to hold your largest peice. Use a V block that alows you to mount pipe between 6" and 8" pipe. Then your Z would need say 10" of travel. This would alow you to run completely through both sides. This would only require two axis of motion.
To operate you would have a stop built on one v block. This would be the side glued to the TEE. Then the operaotr would lay pipe on V block making sure to butt it against the stop. Clamp it down. Enter length then press start. It would then drill the holes per program calculated offsets.
I would use a annular cutter like the mag base drills use.