Yes you can deworm them. They actually should be dewormed at 2, 3, 4, 6, 8, 10 and 12 weeks of age. The over the counter Pyrantal Promate will take care of roundworms/hookworms. Follow the dosing instructions carefully. It may cause diarrhea.
Has this kitten had fleas at all? Or been exposed to them?
If so, you'll want to to treat her for Tapeworms too. Cat Wormers: Tradewinds Tape Worm Tabs for Cats
is a great product and safe for kittens over 6 weeks old. 1/2 tablet for under 4 pounds, you can crush it up and put it in some soft food. Or crush it up, add water and put it in a syringe and squirt it into her mouth.