I don't know if this theory has been discussed, but if you watch the Timeline movie, the part at the end says "this outcome would have come sooner if not for the Republic's less savory allies. I will elaborate on this later."

To me, this screams GenoHaradan. Considering that their goal is to protect and stabilize the Republic through assassination, they fit this profile perfectly.

It could just be a "sith" thing, though organizations like those have been around for thousands of years (even Czerka corp. still exists in the EU) so It wouldn't be a big shock if the Genoharadin were still around 300 years after KOTOR. I don't see them having a huge role in ToR, but I haven't been keeping up with the game's development. It's probably a "sith" or a "gray Jedi" thing.

you should check out the official forums. Alot of people have thought about these less savory allies and most people believe it's simply the republic's class to counter the bounty hunter. Like a smuggler type thing.

Yeah, I think they'll be leaving out the GenoHaradan. The organization probably doesn't exist anymore, at this time.

I was thinking of smugglers, myself, as well. Though I'm not sure the Republic sees smugglers as allies, rather more as a nuisance that is tolerated for the advantages they bring.

Well this is what I got on Wookieepedia:

As of now there is no real information concerning whether the GenoHaradan survived through the later years of the Republic, the Galactic Empire, or beyond, but for centuries there has been no indication of their survival past the Old Republic era. Of course, if they had continued to thrive, then there would not be any indication of their survival regardless.

However, it can be noted that the Tac-Spec Corporation, a droid manufacturer that operated into the last few centuries of the Old Republic, is claimed to have originated as a GenoHaradan front-company. Their exclusive automata for the Republic's aristocracy, such as the FIII Footman Droid, would have been ideal agents for the organization's policy of subtly influencing Galactic politics.

Now one thing to note is that Revan's interaction with the GenoHaradan is "DS", and since the official canon for Revan is "LS" then he never killed Hulas and all those other overseers. Therefore, that reduction in membership is non-canon, so it probably should not be taken into account regarding future survival. Plus, this group survived for millennia already, so the likelihood of them dying before TOR is unlikely.

tell that to the rakata they where extinct when darth bane came lehon 3000 years after kotor 1

Man I have totally forgotten about this organisation, but after reading alittle bit I remembered this from the game! Sweet memories!