Destroying Mt. Weather wasn't the end goal, though, it was just one possible means to the real target of stopping the harvesting and reaping. She was able to do that and free hundreds (I am guessing at that number) of bloodbags and stop the fighting amongst the rest of her warriors and remove the entire reason for conflict between Mt Weather and the grounders, all at once. Of course, I'm sure they would've eventually come into territorial conflict, but that's a much more theoretical and abstract threat. The decision only makes "no sense" if you're being deliberately obtuse about it.
It's a horrible strategic decision to leave Mt. Weather still standing. and relies on Lexa putting her trust in a power that both thinks nothing of the value of their lives, and has the power to utterly dominate them. Once Mt. Weather is back up to strength, what reason would they have to honor their agreement, and what power would Lexa have to enforce it?