Doesn't sound like their compatible. How long have they lived together?
As Kelly said, it'd be best to set up your Betta in his own home. Keep in mind that in smaller tanks, the water current can bother bettas, but that can easily be remedied by adding a bit of filter foam to the inlet and out take valves. I have three bettas - one in a 2-gallon bowl, one in a 3-gallon filter/heated tank and one in a 10-gallon filter/heated tank. In your situation, if the betta is in danger and you cannot set up another tank right away, your fish would be better off in a 2-gallon bowl for a short span.