I really dont think that would work out
If I remember right, one of the few things that we know about the mantu is that they are very xenophobical and territorialistic, which basically was what got the kats and them at war
Now, if I remember correctly, there was some notion that the wcp storyarc would lead to an alliance of three alien species fighting humans and kilrathi, and that the nephilium were just one of those 3, possibly even just the lowest kind
I imagined them as the ground troops that are cheap and easy to produce, and also easy to control, so they were sent to flatten the enemies. As they failled (twice), the other more powerful members of this alliance would come forth to deal with those pesky humans who dared to not just roll over and die
Now, about the other species, I see delance has some kind of hate towards them

The Double Helix could be an interesting idea, if played right. There is nearly no information on them, but the simple fact that someone can have his brains fried by trying to communicate with them make it all interesting already
Now the mopoks, well, cmon, they didnt do it all by themselves...
and, if you want to compare them with ewoks, well, the ewoks have beaten stormtroopers with rocks
Considering there arent that many kilrathi soldiers in that "meanwhile" scene, and what you do to get to that point, It would be easy to imagine those were the few soldiers who remained on the planet, without support. Considering the Mopoks are hunters who live in that planet, they can easily capture some kilrathi with traps and ambushes