Scuttling the pirates is a valid option & I can see at time's this could be quite advantagous, but it is more micro managing which is the the real issue to begin with, esspecially if they begin attacking something and are all scattered all over the GW.
Personally I would like to have the option to accept or decline an up coming pirate fleet. You could still scuttle them if you wanted. Perhaps though this might not be an option because of the implementing of such a thing, IDK.
Another thing would be to simply increase the time it takes before a new pirate fleet becomes available, but I don't know if this will effect the pirates before you ally with them. Perhaps they are set to arrive at the same rate a raid party materializes and a change would effect both.
May be if the ships you want to build were queable before the fleet points are available and over - rid or were spent on the qued items before any points are allocated to pirate numbers.
Come to think of it, at times I am seeing my fleet points values being in the negative perhaps because of ship that is in construction and or qued when the pirate fleet arrives. or perhaps it was from a captured ship or 2, its hard to tell with so much going on. Has anyone else noticed what going on there?