Are you sure this kitten is only 3 weeks old? Are you bottle-feeding her?
If you are sure she is not being hurt or terrorized by your cat, then supervised play periods might be o.k. Does your male cat stop when the kitten "yelps'? Sometimes young toms can get very wound up and do damage without meaning to.
If you see him getting too rough, or starting to lash his tail, pin his ears back, take a stalking position etc. you might want to have a little squirt bottle handy to cool him off and teach him that this is not allowed.
I would be sure to put this tiny kitten someplace - like a bathroom or carrycage - when you go out. Much better safe than sorry.
