Welcome to parenthood!
Well at that age I don't believe you can just let something like that go. But at the same time, it's a lost cause to turn something (anything) into a power struggle. My only two thoughts are:
1. Make her clean it up. Of course you'll still be doing most of the cleaning and maybe she'll be wiping the floor with a paper towel and possibly making a bit more for you to clean. But it will start to emphasize a direct consequence of her behavior.
2. I'm not sure about this one... for an older kid I would suggest giving her a reward of doing something she doesn't get to do often, if she eats without throwing her food. The problem is that won't work if the kid does have a concept to relate action A to consequence B, and if they don't take place at the same time, I'm not sure at her age she will make the association.
On the other hand, ignoring it may seem counterintuitive, but it might be the way to go. Pushing buttons and getting a reaction, even a negative one, can be a "reward" of sorts, and sometimes what you have to do is just not get pissed off no matter how badly you're provoked or how much it's deserved. (This advice is easy to give and hard to take, as my children would be happy to tell you.) But I personally would try #1 first and see what happens.
EDIT: I like Smurf's.