I haven't found Moras to be all that troublesome.
1. They're very easily Flux-pressured to the point they just run their System and spin a lot.
2. They're very vulnerable to strikes by bombers (which are hella good now that they're able to mass and their AI is better- a flight of them from a Drover is pretty deadly to anything short of an Onslaught, fyi).
3. Kill their fighters with hard counters. If you're flying High Tech, you need a Beam Wolf Pack or equivalent in fighters or you're going to have trouble; Low Tech still has Flak (although given the huge nerfs to Captains, it's no longer quite as good) but should actually make use of the Talons and Mining Drones, because one is almost-not-bad now and the other can be spammed without losing Crew.
4. When a Mora has turned on its System, EMP, EMP, EMP.