Before you freak, I've thought this through. The mechanics of dungeon keeper as it stands could support a rogue-like features with some minor modifications.
First and foremost: Procedurally generate maps, just caves. Perhaps you could plot several rooms and connect them by tunnels. This would be fairly simple to do I should think.
Secondly: No dungeon heart, instead have your PLAYER's main creature the IF_DEAD = LOSE condition. There is an important reason for this, multiple-level dungeons.
Multiple-level dungeons could be connected by the pre-existing staircase model. Also, no overworld is required, players can't switch views between levels during this mode. The camera remains on the level the player is occupying.
Leveling and rewards: Leveling can be done by simply fighting monsters. Personally I think it should be a little harder to level your creatures considering the game only supports 10 levels of creature.
Rewards of gold could be found throughout the dungeons and possibly shops in the cave (much like Powder or NetHack's dungeons/caves) that could provide buffs or special items, one-time spells and of the likes.
Movement could be simply dealt with by using the Call to Arms code, maybe even just hiding the flag to make the system appear to be different even though it is the same.
That system also works well for allies. As they would all follow the same call to arms... call. Of course, you want allies to be expendable as to not let the player amass armies of helpers. Maybe helpers don't level up, ever. Therefore they never gain additional maximum health, but if the player needs or wants to they can provide healing to them to keep them alive (healing spell could be a substitute for "potions" or actually regarded as a spell, only sold by magic shops).
The player, I was considering this to be a "playable heros" mode too. Originally I was thinking about playing as evil creatures making a quest to a dungeon (of course never actually having a goal to achieve, instead the game is endless) then I thought, wouldn't it be interesting to play as a long hero, questing into the dungeon lairs of the evil ones. It would provide the players with the ability to play as heros and stay, for the most part, true to the Dungeon Keeper style.
Comments, questions and criticisms welcome.