Quite honestly, whatever explanation for Vitiate not attacking they could give (both the one that was effectively given, and the ones they could/should have given) would not be believable, because the KotOR plot has so many loopholes. Regardless of Revan, Vitiate should have attacked during the events of KotOR 2, when the Republic was in disarray and there was no Jedi Order to protect it. The reason he did not is a mystery, a stretch and a majour loophole. So that situation really could not be salvaged in a believable manner.
But on the case of Sith destroying Sith, I would oppose that spelling doom for Vitiate and his empire, seeing as that is what ends the New Sith, and that pertains to the prophecy of the Sith'ari, the Dark Lord that would rise, destroy and recreate the Sith in his own fashion. Darth Bane fills that role, so he's got the dibs on that approach. I would much rather see the relationship with Vitiate's Empire and the true Old Sith Empire developped, crippling the Sith Empire, but its final end should come at the hands of the Jedi. It would be a nice closing, too, since all the other wars in the Old Sith Wars were ended by the deeds of the Jedi.
That's why it should be destroyed by the Sith, or at least caused by something a Sith/multiple Sith did. The problem is they made too many of their characters too op. Vitiate, immortal. Nox, immortal. Revan, never dying. Scourge, immortal. That in itself causes inconsistencies.