Kirsten I think that is just awful!!! My mother is an animal lover but I can relate with the bf thing. We have been through many and it is awkward when you really don't want them in your house. What he did is not only mean to Lily but it is disrespectful to you. He knows how you feel about her and that is why he did it. I truly don't think it had anything to do with Lily. For some reason some of my mom's bf's have also wanted to show some type of power. It's like your a little kid again and they think there is nothing you can do about it. They know you don't want to have problems with your mom so they take advantage of that.
If you confront him he will say your acting silly because he didn't hurt the cat but was only playing. He will try to make you look like the nut. My mother is currently married to man similar to this now. He is husband #6 so I don't know how long he will be around. He has never done anything like that to my cats but he has made comments that he knows will get a rise out of me. It is all about control. He is a control freak. At least once a month he pushes me to see how far he can go. Thankfully for me this current guy has stopped right at my snapping point. He knows it and I know it. It's like a game that they play and you have to stay one step ahead all the time. I finally quit playing and tell him exactly how I feel right there on the spot.
I wish you the best of luck. I'm sorry to ramble but you hit a nerve for me with this subject.

On a happier note...I hope your back feels better real soon. Sending PT prayers that you will have a quick recovery!!