I think I get your premise - basically you want to help prevent a player from simply quitting because all the work they've put into the game is suddenly gone. Correct? That's why I like the idea, and honestly I probably wouldn't be bothered by the auto-regen should it be a small amount or capped out.
So, if a city started with whatever amount of infra and is taken down to less than, say, 1k it could auto-regen to 1k and the rest would have to be built up. If the player purchased infra before it got to 1k, surpassing the 1k mark, the auto-regen would cease. Regen rates could be smaller like 1% per turn or something so that people aren't just sitting there to save that tiny bit of money anyway.