at the end of M1, he had a choice but he was compelled to stay, compelled to disobey. he was obsessed with one thing- destroying neo. he still had the choice to return to the source or not. he didm't wanna be deleted. he knew that that's his purpose but he wanted to kill neo. in M3 the source "went" to smith through neo... thus negating the possibility of a return of the same exact smith because he was already deleted by the source.