Well, first of I'd say that the inhabitants of Metru Nui probably weren't that eager to get help from the Brotherhood - let's just remember how Teridax "pacified" the city the last time - locking everyone who wouldn't put down their weapons in the Archives and letting Rahi loose on them.
Then Teridax might have been the Makuta of Metru Nui, but he also was the leader of the Brotherhood and thus Makuta of Destral. I deem it most likely that Teridax wasn't even in Metru Nui at the time, but instead took care that the preparations of taking over control of the Universe would proceed.
Most importantly, though: Let's say the Dark Hunters would've won. What then? All Toa of the city would be dead or imprisoned - exactly what Teridax wants. The Matoran would be put to work - exactly what they're supposed to do. The armies of the Brotherhood far outnumber the Dark Hunters - if they should have any problem with the Makuta taking over the Universe they would be crushed. After all the sole reason why the Brotherhood of Makuta - Dark Hunter "War" after the Great Cataclysm went on for so long was because the Brotherhood didn't pay much attention to it. I mean, the Dark Hunters couldn't really hurt the Brotherhood as a whole - if they had tried to take Destral they would have performed suicide.
I'd say Teridax didn't really care about Metru Nui as a city - he let Turaga Dume handle everything until it became time to take matters into his own hands and then simply put Dume to sleep.