Howdy,
I too had one aptaisia in my first tank, and I let it grow because I thought it looked cool and it did not reproduce for a long time. Unfortunately it finally sprouted offspring, which immediately took over my tank.
The only method I found to really get rid of them was the Kalk injection. I also added a twist to the procedure. I would boil some water in the microwave, add the Kalk, and inject it directly into the hydra's mouth using a syringe. The double assault of Kalk and boiling water killed those ugly mutha's right quick. Never had a problem after that.
I think if you can get the syringe right into the mouth, you can avoid hurting the corals on either side.
Good luck,
Scott.