You say you'd hate him to get fired over $3 but he just proved he wasn't a trust worthy employee if he is stealing from customers.
He gave up his honor thus you must give up his job.
Bingo. Doesn't matter if someone stole a candy bar or a new computer- stealing is stealing.
I remember I ordered one medium pizza and an order of cheesy bread with my cousin from Dominos, and the delivery guy told me it was $24 bucks, and I was like oh.. man.. that's all I have I'm really sorry, so I just gave him that in cash with no tip. When we got inside, we looked at the box and the total printed on it was $13. He literally screwed me out of over 10 dollars and gave me a judgmental look when I couldn't tip him.