You used 3 terms here, which to the uninformed, could well be used interchangeably...account, membership, subscription. You know this system well, and obviously, are doing a good job in trying to help. But put yourself into the position of a Yahoo Form member who just got moved to Groups, and likely doesn't even really understand why (even though they have been told Yahoo is imploding) nor understand anything about Groups. You can not expect them to understand the difference in terms without some explanation. So you are right, I think the distinction between them need to be explained more clearly for the user, especially during the initial process for the new user.
It sounds like from your note that the system was intended to send the Pending message after the person replies to that initial message. That would help in the process greatly, but as J pointed out, that is not the way it works for a web application. Resolving that will go a long way in resolving this whole problem. But as John mentioned above, it would be nice if the message they received was customized to the group they were becoming a member of, and even nicer if we could add to or modify that message since it will be the first message they receive from Groups.