I don't see how it could be worse. The fuel storage pool is a quite robust structure. Not as strong as the containment building but no pushover. Sure, it contains spent fuel, but in general it has undergone quite a bit of decay. I may be wrong, but it is my sense that the source term for a storage pool release has got to be orders of magnitude smaller than for a core that has reached equilibrium burnup.
Impact would be the primary mechanism for storage pool damage. Fuel elements have very high melting temperatures. The zircalloy cladding would not weaken even at sustained high temperatures like you would have in a jet fuel fire.
Plus, it would be just damn hard to hit the thing head-on. You're talking about targeting a specific structure within the overall plant, not just plowing into the side of a building or smashing into the general area of the plant layout. Its possible, sure, but a cut above the difficulty of landing in the Pentagon.
I doubt even an experienced pilot could pick out a specific small building within a complex such as Three Mile Island. And then hit it head on.