From what I read it isn't really known if he knew that he assassinated Lincoln at that point. He had met booth prior . At that time Booth was a fairly famous actor.Were they? Did they already have the news that Lincoln was assassinated? Or did he just show up on his doorstep for help. I've always wondered about that. (This is a legit question)
So considering his house was somewhat isolated, his family was in the house and he had his cousin notify police that Booth had been there I can make the assumption that he did what he felt he had to.
Even if this is wrong and he was a coconspirator, his house is still part of history. I had never heard of Samuel Mudd until I moved here and the sign made me look it up and learn more about Booths attempted escape.