User blog comment:IamJakuhoRaikoben/Chapter 459 & 460: Weakness & The Alighted Pegasus, Review./@comment-26287497-20151102053120/@comment-7418318-20151102230907

True, it's their best way to shoot down the air-fleets, but if they are driven away from the cannon, it means that a sizable body of troops must have landed already and thus there's not much point for having it anymore and there's alway the "better destroy it than letting the enemy use it" matter.

But on the other hand, Alvarez wants to capture something within the guild hall, so they can't fire Jupiter directly at Fairy Tail, which greatly reduced the risks of letting the enemy have it. There's always the chance that they can retake it later.

Maybe taking out a key component from the firing mechanism would be a good choice, since the cannon couldn't be used that way (it's unlikely Alvarez has spare parts for a Jupiter cannon with them), but could be made usable quite quickly again if they manage to retake it.