have to agree with the other commenter, a molly in a 2.5 gallon (or under a 5 gallon AT LEAST) is not good. usually no fish is good for a 2.5 gallon which is why they are mainly used a shrimp tanks. Water quality in that small of a tank inhabiting fish is very difficult, and hard to maintain steadily. I suggest you donate all the fish inhabitants to an lfs or forum member, someone who is willing to care with proper conditions.
As for the filter issue, I suggest until you rehome the fish, to get a window screen and cut it into a reasonably small piece. Then put it around the filter intake, using rubber bands (or similar) to keep it on tight. this will however require you to clean the intake more often.