First of all, CONGRATULATIONS on having a 2.5 year old that not only is potty trained, but even gets up to pee! that's AWESOME! Know that you are in the minority there!
As for the sleeping issue, you could try putting him to bed a little later if you think that would let him sleep a little longer. Would he be content to watch a little early morning tv snuggled up on the couch while you exercise? If not, I would probably just continue to do what you're doing, laying with him until he goes back to sleep, and just do what you have to to stay awake, or set an alarm to wake yourself back up. I use my cell phone's alarm, and keep the phone on vibrate under my pillow, and it always wakes me up, but doesn't disturb my son.
Best of luck!