Well my server would like to disagree with you, this mess was caused by my brother, and it actually dragged the server down to an unusable state. He didn't know, and I didn't know how to help him, which is why I originally came here to begin with.
My experience with Tekkit was pretty limited and I hadn't used things like the filler before, and I didn't even know they existed.
Yes I can totally agree, you do.. you DON'T want a mechanic of the game to crash your server, which it did in this case. Causing it to be unusable for a lengthy period of time until everything finally catches up. Especially during the draining process.
I did use the filler to fill in the area 8 blocks deep where all the water sources where and then some just to be sure of the deep spots in the small bodies of water that were there when my brother built the thing initially. All is well now and we're all the wiser.