Usually he needs you to be in contact every now and then before he runs on. Just check your quest arrow and when it is red he has usually stopped somewhere along the way.

Regarding the guards I think that with all new try-out-characters that I have made everyone except the high level one has more or less finished with all but one or two dead. Last time one fell by mny sword when he jumped infront of me fighting a skamp. I yielded quickly to his friends and thought, alright, assasin initiation started ;) . Not until I entered a city with guards did I understand that in this game, information spreads lightning fast and everyone knows who you are. (It is really a wonder that the guards haven't stamped out criminality yet).