The ship is equipped with a transporter that has adequate range but cannot get a 'lock' to transmit or pick up anything within of the living vessel. Karnak's ship's armaments include anti-matter bombs, about 5 times as powerful as a single H bomb but 'clean', and a force beam array. The bombs dentonated within a few miles out should, at least in theory, do quite a bit of damage, but targeting may be a problem. Melanoce may be able to get a hold of more powerful weaponry and have teleported out to her within fifteen minutes, but would require negotiation wit bureaucrats.
The party is only about a quarter mile from the exterior of the living vessel, but a route hasn't been scouted for that. And you don't know if there's anything like an airlock available. Melanoce's route to where the mirror's sensor is located seems straightforward, but there were several groups of entities in the way when the path was scryed.