Well, reducing captured cities to ruins.. that would mean a scorched earth trait, and Diesel is right about that being out of character.
I'm not terribly sure how unbalancing allowing captured cities to remain standard cities would be really. The super cities are nice, but you are limited to a fairly low number(2-5, depending on map size, and 5 is really not many considering just how big a Huge map really is). Once you hit that number , you are limited to settlements anyway(for new built cities).
The major liability to them is that Domination or Conquering on large or huge maps is really difficult because you can't(easily) strategically place forbidden palace or winter palace, making maintenance really a pain(Though I suppose settlements don't have a maint cost, but waging wars across the world is tough).
What if we dropped the cap of super cities so that 3 was the Max, and captured cities had a pop up of only settlement or standard cities? That would make the core of the Empire solid and Sprawling, but leave them room to grow.
Actually, had a second Idea. What if settlements were expanded a bit. Put them back into the City Maintenance count, but allow them to build a limited number of other structures. For example, you could build an Archery range, OR training yard, OR stables.A small settlement should be able to support a single "conscription" type. A market isn't unreasonable in a settlement, nor a Pagan temple. Maybe a Forge. Perhaps allowing them Wonders(some of the most ragged little villages have sustained only because of some particular Holy site or war monument, so its not unreasonable), and with the Settlement building hits, it would be risky anyway to try to build one there. Just thinking out loud here...
Cheers!