I think I have come up with a simple and compact obsidian generator design (7x1x2). At the minimum, it requires the following:
▼÷÷.÷÷▼
≈█████≈
One liquid is water and one is magma.
This can be tiled indefinitely. Power is transmitted between adjacent pumps, and liquids flow between adjacent intake channels.
You can operate the pumps with dwarves, or you can set up power. If you use power, it might be possible to make a power-switcher to give each pump a single tick of power. Perhaps a repeater with multiple pressure plates, each connected to a gear assembly? (The wiki says that gear assemblies respond to triggers immediately, so that should work.) This would decrease the power requirements, but at the expense of a repeater.
(Edit: Wait, no, they transmit power. And if you leave rows without pumps to break the power transmission, then you might get a tile of magma that kills your obsidian retrievers. Maybe have doors between pump sections?)
The activation is simple. The pumps on both sides activate at the same time, pumping water and magma into the same position. If the pumps are accidentally left on, there is no harm so long as they are deactivated before you start mining the obsidian. This design has no risk of flooding so long as the ends of the outtake channel are "capped" with a door. To mine the obsidian, simply unlock the door and designate the column of obsidian for mining.
(I can't tell if this is an improvement over the standard "pump water over magma" obsidian generator.)