Yep, definitely a security issue. I would have shot the intruder dead, therefore making him very easy to locate. Not sure if a concealed weapons permit is a valid option for your friend, and regardless it won't help the current situation, but it does provide a feeling of security in case that were to happen again.
J-M, I have nothing against guns (I've got a shotgun and a pistol at home), but I'm curious. There are so many incidents of the hotel issuing a new guest a room that is already occupied, don't you think it might be better to ask questions first and shoot later? I've been glad for my shotgun at least once when someone tried to break into our home (I didn't need to fire it, but keeping it trained on our bedroom door while waiting for the police sure made me feel a whole heck of a lot better about the situation). That time, I was prepared to shoot through the door if the knob turned -- no one had a key to our house, except me and my wife and we were both accounted for. However, in a hotel, likely as not, it was just some room clerk screwing up (though probably not in the case of the OP's friend). You wouldn't really shoot some poor business person who had the double misfortune of arriving late and being given the wrong room, would you?