How about a bunch of those point-ships, you know, the almost-no-model ships they use for machinima and blind targetting, invisible to the naked eye? Equip them with like 4 phasers with sufficient arcs. When the weapon is fired, position how ever many of them at points around the ship and have them fire continuous beams at each other, creating the web.
The point about gameplay is a good one, though. KA had an ingame web weapon, though as I recall it was more of a momentary inconvenience than an episode-long handicap.