Brie, what are you referring to about the "paid through date" being overridden? Are you referring to the "Membership Expiration Date"? This date is only automatically updated once the invoice is set to Closed. Adding payments, such as installment payments, will not alter the Membership Expiration Date.
The initial thought process regarding Deferred revenue was to essentially divide the payment(s) among the duration of the membership. We would expose these payments via Custom Reporting so you could run a report for the month to get a list of payments to claim as revenue. This 'report', however, needed data that was not currently stored in YM such as a second GL Code and a way to total per GL Code of what should have already been recognized and how much to still defer.
I have been trying different avenues to gauge the priority of this feature but to no avail. While this feature would be nice I am not getting the sense of urgency for YM to update the commerce features to include breaking down the payment and adding code to the reporting engine that would allow multiple totals.