Replying to the message does not activate the account if it is a restricted group. This is misleading the user, ...
Actually it does activate the account. An account is not the same as a membership.
What it doesn't do is approve their membership in (aka subscription to) your group. I think what you're looking for is to have that distinction more clearly made.
Maybe a better option is to send out an email to _just _confirm the email address, and then once that is received, send out the group’s Pending Subscription message. This would present a more logical flow for the user and give more control of the communication with their users.
Please explain how your proposal differs from how it works now. The Pending message is deferred until after the person replies to that initial message, or clicks through the link to Confirm their account.