Your first diagram is EXACTLY what I did. Sh*t. I'll have to try doing it like your second diagram. Does it still work if there's a staircase to the surface at the top of the "hump" in your second diagram, or do I have to do it all sealed?
Since you're dumping the water into an aquifer, ordinarily I'd say it'd be fine. But the initial point when the ocean drains is probably still going to flood -- if your staircase is under the top level of the ocean, I would imagine it would flood. If it is at the same level or higher than the top level of the ocean, you should be fine.
But, when in doubt, put a hatch cover on it.
Edit: And is there a way to arrange it with gravity feed instead of pumps? Or, if I do use pumps, I wonder if with enough pumps running full steam before I open it, if they can keep the water low enough to allow a miner to survive breaching the ocean floor?
With a gravity feed, any levels of the ocean that are at the aquifer level + 1, or lower, will not drain. Referring back to my diagram:
XXXXXXXXXXXXXXXocean
XXXXXXXX _Pp Xocean
XXaquiferX pP_Xocean
XXXXXXXXXX Pp XXXX
XXXXXXXXXXXXX___XXXX
If you removed the pumps, so it was like this:
XXXXXXXXXXXXXXXocean
XXXXXXXX Xocean
XXaquiferX Xocean
XXXXXXXXXX XXXX
XXXXXXXXXXXXX___XXXX
Only the top layer of the ocean would drain. The layer immediately above the aquifer, and everything beneath that, would not drain, because it would not flow over the "hump" into the aquifer.
If you want to do it by gravity, you could try digging a shaft to a level lower than the ocean, running a tunnel to the edge, and then smoothing and carving fortifications into the edge-of-map tiles. This should give you an infinite sink, but I'm not sure it'll drain faster than the ocean'll fill. You could try something like this:
XXXXXocean
XXXXX XXXX
XXXXX XXXX
F XXX XXXX
X XXXX
XXXXXXXXXX
(The point of the u-bend is to take advantage of the pressure physics -- it should give you the maximum amount of drainage.)
(Do be warned that sometimes carving fortifications on the map edge results in an infinite *supply* of water.)