I would not melt the Warlock for any reason. Sell it if you must but don't destroy it. It is not available, and the EMP could easily become a rare item. They were distributed in concept and they're flight ready, but that does not mean the ship will ever be available again.
The EMP generator is obviously meant for a different kind of play than what is available now, but this is reason to suppose it will not be available later. Should they never offer it through normal sale again, that item could make the ship worth many times what it sold for originally. certainly those items are treasured items for anyone planning piracy or privateering.