Did you ever get an answer to this? In our own preference center, when someone unsubscribes, we remove them from all of our preference center email groups, so that, as you mention, if someone is resubscribed, they don't automatically start getting emails from different email groups. If you don't have a process like this, then a program that runs daily sounds like a good alternative.
We use program builder to override the unsubscribe for our transactional emails. It is a royal pain, and as you say, creates a complicated and decentralized workflow. But we have many transactional emails that happen from form submits and inside campaigns, so there isn't an effective way to subscribe the person, send the transactional email, and then unsubscribe them. I have submitted a help desk request to return the unsub override to all email send processes. I hope to see it soon, but don't have any commitment from Eloqua for that yet.