Matt,
Georgia Tech is one of the major sponsors for the Peachtree Regional and the Georgia Tech FIRST group (a group of undergraduate students) help run the committee and the team recruitment effort. We participate in the Peachtree regional with our team, the Circuitrunners team 1002, and even won the regional and the regional chairman's this year. We did not receive any backlash for it since others saw that the team deserved it.
I definetaly say that you should participate in the regional that your team will help run. It's great to be able to participate in the regional that you put so much time and effort to plan and get going. It seems that your situation is very similar to what ours was about 2 years ago so if you have any questions, let me know. Good luck and have fun with it

.