The absolute need for a full set of crystals is a bit curious in "The Alternative Factor". The ship seemed to achieve much greater things with just one (cracked) crystal in "Mudd's Women" than mere "hovering for ten hours above a planet"!
We might argue that Kirk isn't really worried about losing a fraction of the crystal power - but rightly concerned about what actually
happened, namely the total
loss of active dilithium crystals for the time being. Lieutenant Masters got four of the crystals nurtured back to health reasonably fast, which might eliminate the risk of a fiery descent; the repeated thefts and sabotage would complicate things, but there could still be more than four paddles in all, and enough time and enough energizers to restore power to all of them.
Certainly the idea of restoring power to the crystals speaks against the idea of the crystals themselves being the ship's source of power; they seem to be recipients, rather. The idea of them acting as a medium of transfer gets reinforced in this episode in many ways.