Just recently I was running what could be called a raid encounter with two groups of fleet mates. It was the Crystalline Entity. We managed to get the boss down to 30% health at which point a group of other players entered the encounter and started to purposefully grief us by engaging the large fragments and shattering them so that they would heal the boss. This went on for almost 45 minuets before the group leaders called off the attack and everyone left the encounter... in that time we brought the entity down to 30% at least 5 times. we would have completed the encounter had it not been for the interference of the other players who when asked to stop refused to do so.
The only way I can think of to prevent a situation like this in the future is to implement some kind of Raid Group interface. Increase the encounter limit to 30 players and allow players to put together a raid force of up to 6 full groups. Then lock the encounter so that ONLY those in the raid force may enter.