I think some kind of anti-phase system would instead make sense for some new midline cruiser. Some kind of phase interdictor that forces phase ships to unphase and prevents them from phasing in for the duration. Might be an interesting system for designated ECM ship. It might however also make sense for system to be indiscriminate should it be AoE of any sort - your own phase ships will be just as affected as enemy ones.
Alternatively there might be a starsector analogue of depth charges often used by destroyers IRL to deal with submerged submarines. Maybe there could be a specialised version of Salamander that can phase in and specifically target nearest phase ship but is useless against normal ships or phase ships that are not phased in.
