Since jump engines can take as much as 20 Minutes to recharge (as seen in several episodes), using them as Weapons is usually rather Impractical.
Considering the energy requirements, it's a bit like the old "Sledgehammer for a Flyswatter" analogy.
Plus, the jump point forms pretty close to the ship generating it.
That would mean the ship using one as a weapon would have to get into "knife range" before using it.
Giving the Target ship plenty of time to blow Lots of Large Holes in the ship trying to use its Jump Engines as a weapon.
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Do not ascribe your own motivations to others:
At best, it will break your heart.
At worst, it will get you dead."