He’s trying to cheer her by being absurd: “Man, witches have gotten weak. In the old days, they wouldn’t have anyone get away with that. They’d pick up the whole town by that tower and stick it on some mountaintop or something.”
あの塔を持って pick up the tower
この町ごと including the whole town–〜ごと means “including…” or “…and all”. See also まるごと which means “the whole thing”.
どこかの山のてっぺんに a mountaintop somewhere
でも …or something, not necessarily a mountaintop
乗せちゃう put on, with 〜ちゃう marking this as unfortunate (for the town) and definitive.
んだけどなあ a better grammatician can probably explain this, but I think of it as “a pile of particles tossed on the end of the sentence to soften it or make things flow better”.