While the marauder does have the BEST way to counter an incoming MB, the vasari do have another alternative. I do believe the kortul's disrupting strikes can intterupt the missile barrage, I am, however, not completely sure about this, as i've never tried it.
As for the stabalize phase space ability, i've never really used it as a assault ability. what i have used it for however, is to bolster up my defensive fleet when i need to. I link most of my key worlds up with stabilizer nodes, and have my main fleet out wrecking havok on the enemy worlds. If i suddenly get attacked, i'll have my marauder fire up its node and then my fleet (except for the marauder of course) can jump back to the world that is getting attacked to defend it.
If you are set on using the ability to get by a chokepoint or something tho, you miiiiight be able to do this.
1. send your marauder to the world you wish to bypass, and then activate gravity distortion to get through it really quickly.
2. jump to the next world, and when you reach it, fire up the node and send in your invading fleet.
this of course wont work if there is a starebase in the system you are bypassing, because you wont have any antimatter to use the node when you get to the next planet. It's probably much better to just use the vasari supercannon to make a node to jump your fleet to.
hope that helps you out 