Sovereign has a point about system resources, but I don't think that's insurmountable.
For example, your phaser-ships needn't be probes. You could use those single polygon invisi-ships that screenshot artists use. Lurok91 and I were discussing a similar idea in his Mutara Sector thread. They would be much more resource-friendly.
I think the hardest part is going to be the flocking behaviour, to get them to surround a ship in a geometric formation. If you manage to tackle that, it could probably be adapted and applied to fleet formations, too. It could come in very handy.
One suggestion realting to that is that, to immobilise the target ship, one (let's call them nodes) node is armed not with the thread phasers, but with a weapon similar to the Breen Energy Dampening weapon, it would shoot the target ship every once in a while to keep it from moving. The weapon should be silent and invisible.
I actually think this is a great idea, I think it was had before, but that was a few years ago, and things have since been done in the game that were then thought impossible (wormholes, for instance ;)). The biggest stumbling block, as I say, is the positioning AI.
Unfortunately, I'm not much of a scripter, so I can't help you there.