Your BIL was "projecting" and most likely do the pilfering himself. He wanted to be able to do whatever he wanted, whenever he wanted and figured your h wouldn't care since he's not around. He wanted to get rid of you because you were there working and would see things. In other words, your BIL was a very jealous man of both you and your h.
As for your h taking care of his brother, his brother is a grown man and should be able to get another job. In fact, he needs to get in the unemployment line and start looking. It is not a family obligation to keep a sibling on if he/she isn't working out. I wouldn't be the least bit surprised to read later on that a lot of stuff went on that you didn't know about when it comes to your BIL.
I'm glad you and your h had a good conversation about the situation and I think all of you will be better off w/the BIL gone from the business. As for your H's family, they'll either get over it or they won't...but it's not their business to operate. It's not too often that siblings working together in a business that is owned by one of them works out. I have seen this happen before w/my xbil and xh.
Hang in there. I think you and your h both did the proper thing. Don't give it a second thought.
Sit quietly, the answers will reveal themselves when you least expect them to. The past is gone, the present is a gift and you need to focus on today, allow the future to reveal itself when it is ready.