Modded maps can substantially alter any unit/building/tib stats.
This isn't entirely true. As a fellow Halo fan (and MLG alumni), there have been forge (Foundry) based maps that have made it into playlists - created by and for MLG of course.
Outside of that, I'd never propose for conf or visc maps to be added alongside to any ladder with WW maps. That'd be mental... I do however, have a special place in my heart for BBG and wouldn't want to completely shut the door if we ever decided to "expand" on the map pool via official map pack. I wholeheartedly agree that maps with infinite tib etc., have no place in the same ladder as traditional style WW maps; so, I'd probably recommend two separate ladders (one for WW maps; another for [certain] mods).
With that said, I certainly understand the security concern regarding a ladder for mods maps. However, with the tech available through CnCNet, we should be able to limit which maps can be played officially and prevent malicious users from playing altered/non-sanctioned versions. This would be extraordinarily difficult through any TS WOL emulator/implementation, so thankfully we now have some room to think "outside the box". I just don't want us to fall into the mindset of, "that wasn't possible there, so it won't work here".