I'm trying to dig down through an aquifer in deep winter and my dwarves keep getting frozen into the blocks of ice. I've tried designating the channeling in different manners, but I can't seem to keep them from digging out the area and then jumping in right before the water from the surrounding aquifer squares flash freezes.
You hopefully have a burrow defined that encompasses your fortress interior, for sieges and whatnot? Try extending that burrow so it covers the current surface of the aquifer, but not the z-layer beneath, and set the civilian alert level to restrict to the burrow. With a little luck that will cause your dwarves to treat the freshly channeled-open hole as forbidden and avoid jumping down into it.
You could try carrying out channeling in summer only; the water might freeze more slowly then.