I think they need to act smarter. You don't want to have 6 of them all fire on one trade port if it only takes 2 or 3 to kill it. You should be able to queue up targets for them, but right now it seems like they can't actually target structures, you can only use the ability, but you can't use the ability for the fleet when it's grayed out, even if one or two of them are ready to fire. You have to go hunt for the ones that are ready and then tell them to use their ability to attack.
So, we need the ability to queue up targets just like other ships, and have the AI understand that it doesn't have to make all of them fire at the target, just enough to get the job done. They should only overkill by a little, not a lot. If it looks like it would take 2 of them to kill it, then have 3 of them fire at it just to be sure. The other 3 can hold off, and then the group moves on to the next target and the remaining 3 can hit it (assuming that's how many the AI determines are needed to kill it). The remaining 3 shouldn't move on to the next target until the first one is dead though. It could take them into range of the first target (assuming it's a turret or something else that shoots).