Detonating an omega molecule would be a severe overreaction, wouldn't it?
Sure, it would keep enemy fleets from warping around in that area, but long after the war is "over", no one
can go warping around in those areas. That's not a good weapon of war
- that's a weapon against civilization
! It'd be like deploying a weapon that would render ocean or air travel impossible.
As a matter of practicality, though, how would the omega molecule be used? I don't recall much about it, but can it be transported? It would no good to "build" it on Earth, only for it to explode in transit. Better to create it at the site of use, then - but how long does it take to synthesize one of these monsters? Days, or years?