How do I politely ask my roommate to get rid of her cats?

True friends stand by you. Superficial ones don’t. I know this from first-hand experience, 25 years down the road from sorority life.

She is not a friend to you doing this. Why do you owe her something that she is not giving you (basic respect and courtesy?)? Friendship is a 2-way street.

If it were me I’d draw a boundary line. Give her a chance to resolve the problem (i.e., move or re-home the cats and treat the fleas) or I would take some action.

You’re not being unreasonable or mean. Not to mention the poor kitties who deserve better.