Well as a quick and easy measure you could get a pair of tights or stockings (new would be best, so the cheapest ones you've got), cut the foot section off and tie that around the inlet holes of the filter to stop the fry getting into the filter but not to stop the filter from working (fine mesh/stockings won't block the water from being sucked in so should be ok). Oh, sorry, I'm assuming you're female LOL and would have such items in the house!
Having said that, some fry actually do well living in the filter for a while as they can hide away from bigger fish for a while and nibble on the food debris that gathers on the filter sponges. Only problem would be if they grew too fat to escape back out of the filter!
As for food - yes, you should be able to feed them on crushed flake food, that's perfectly fine for them.
Athena