I have never done the Pipe Organs, but I would probably break or cut using fragging cutters, maybe even a thicker type razor blade would be better. Cut it between the individual tubes, not trying to damage the tubes themselves. These can be hard to keep for length, so I don't know how well they will handle being fragged, but I guess as long as water quality is good and you feed the frags when they perk up, they should be OK, IMO. Is it a healthy colony or one that's on its' way out. Hope this is a little helpful, again it is just what I would do if I was doing the fragging here.
Matt