There's nothing wrong with using your STI levers. I wouldn't just because I'd be afraid of accidentally wrecking them and being out a couple hundred bucks. If you do decide to swap out for a set of aero brake levers, look around for the fattest hoods you can find. Shimano has really nailed the ergonomics for riding on the hoods. Cane Creek has some that aren't as nice as STI but are much better than the classic aero brakes.
As for pulling off the rear brake... Eh. Do whatever you like. If you want two brakes, ride two brakes.