with the exception of the waterbottle boss's welded on, you've got plenty of room for a motor.
i think, though, that you've already answered your own question. if you feel that putting a motor on it is going to "mess it up," you should get another bike.
the motor and all it's components bolt on, and can be unbolted, too. meaning, the most that's gonna happen is you'll scratch it up, spill gas on it, probably torque your back wheel out of true, and worse case scenario, crash it and really "mess it up."
my opinion, is that it would make an ugly motorized bike anyway, so buy something used and cheap off craigslist, make all your mistakes there, then build something better.