What's in the bowl?
Is your bowl cycled? I'm guessing not... As it is supposed to be quite difficult to maintain the nitrogen cycle in less than 5 gallons. You would have to have a filter for it to be cycled...
So answer is no, you can't vacuum too much and you probably want to do full water changes and rinse all bacteria off of your gravel when you have a bowl.
Bad bacteria can accumulate and cause fin rot if you do not throughly clean the bowl, plus the water will just end up accumulating ammonia, which will burn the fish's gills etc.
You could always get a 5 gallon, a heater and a penn plax small wonder filter. Then do a fishless cycle with pure ammonia before adding the betta:
http://www.cichlid-forum.com/articles/fishless_cycling.php
You don't have to have seeded gravel etc, since the bacteria are present in the water. Seeded material just speeds the cycle.
I assume you have a betta, which is why I say 5 gallon... You could go larger too. They are super active in a larger space with a heater!
Or keep the bowl and check out bettatalk.com
http://www.bettatalk.com/housing.htm
Oh, and if you don't like the look of a tank, this is what I have:
http://www.amazon.com/gp/aw/d/B0069RTFB8
It's a 5 gallon with no black edges and curved glass corners in front! I got mine for $30 at Meijer though.. The filter it comes with is WAY too powerful, FYI. It would cause one dizzy betta. Don't know what they were thinking including it. I got the small wonder filter that runs on an air pump. It's been cycled for 8 months now. I do not change the cartridge. You can cut it open and rinse the sponge in dirty tank water if needed and then add more charcoal (if you want chemical filtration).
Then with a truly cycled tank, you can just gravel vacuum and top off water once a week using dechlorinated water and water of the same temp as in the tank.
Hope this helps!