Edit: God damnit. I missed this one important bit of your post:
...so that the surface of the water comes right up to floor level.
Leaving my post in here because I spent the time writing it, but doing the above requires a degree of precision with flowing fluids that I'm not at all comfortable with.
As any post of mine that deals with flowing water, I'm compelled to make an unrelated suggestion:
Use diagonal bends at the top of the waterfall to prevent pressure from being a potential problem. It doesn't behave as it does in reality and so it's better to eliminate all potential risk by killing it completely than attempting to guess how it'll behave in practice.
Personally, I never design waterfalls that collect near areas that receive any traffic. That is to say, all waterfalls end in their source cistern. I do this for precisely the reason you brought up: It's a pain to deal with the water pooling after it falls. There are definitely systems that *can* be used, but I'm simply more comfortable/confident in the multiple layers of defense built into my cisterns. If I'm going to design a waterfall with water nearby, I'll just put in a non-flowing pool and leave the waterfall to continue on it's way to the cistern.
With that being said, you do have a couple of possible options, but I have nothing to gauge how effective they'd be in practice:
Option 1 (Probably the safest of the options): Drop the pool down a z-level.
Side view:
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#~#####~#
Water will definitely pool up in the buffer level, but with adequate drainage it shouldn't* overflow. You could also add additional drainage on the buffer zone if you feel like playing it even safer (Although, more realistically, if the extra drainage were to be used, it'd simply mean that you either have insufficient draining on the bottom level or your plumbing has gotten clogged somewhere).
Option 2: Remove the buffer level in the above option and install grates surrounding the pool.
Side view:
_ ~ _
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The overflow will definitely be used, but surrounding the pool completely should* prevent the dining room proper from being muddied.
*Not actually guaranteed to work. I am not responsible for any drowned dwarves or any damage that occurs as a result of any friends or family members of drowned dwarves tantrumming.