zone doctor vs. LE Rogue

Now when it comes to corruption, will deleting unused rooms to save space for tile editing corrupt the rom?

You could use FF6LE for this specific task. However remember that as an example if you are deleting rooms on Narshe interior on map $18 you are impacting maps $19 to $1E. You have to be careful. Also the rooms that seem garbage on some maps are actually used on other maps with a different tileset.