And this is why I love aquifers! 100% secure, infinite source of water right where you want it. Easy to set up and forget. I just leave it "on tap" into my 2-zlevel cistern. The flow isn't strong so it won't flood, and there is no way something can get into the fort through it. It was even a side-tap to an aquifer, so it was insanely easy to set it up and then dig out the hospital (from stone) over it. Yes, they can be an extreme pain to work with. However, once you get the knack for it (keep the wiki guides open in another window) its not so bad. Its especially nice with mountain aquifers, as smoothing stone also stops the waterworks. I had a 9-level aquifer once, but it was no hassle at all to pierce it because of this. The last level is always the trickiest (so reveal to know the depth, or meticulously check each time you go down a floor), but smoothing really makes it go so much faster.
To the OP's actual concern... about the best you can do without shear amounts of brute force (try forbidding water buckets heading to a pond zone, then forbidding them as they are being hauled. Then set up a bucket stockpile and hope the filled ones get in) is to simply set up a bucket stockpile near your well/water source. They won't be filled, but they'll be right on hand near the water source to save time fetching a bucket first.