Okay, it sounds like she knows she is not supposed to throw food since you already went down that road. So now she's testing you. I think you are right about taking the food away from her. Maybe you can teach her something else, like asking to get down - whatever her vocabulary allows. "Down please" or "all done" might do it. If she throws the food, she does have to clean it up. If she gets hungry, then she goes back in the chair with the SAME FOOD. That's important! Dinner is dinner, and this is what you are serving. Of course you are offering a choice and you are going to make allowances for trying a new food and not liking it. But you can't keep putting her back and offering her new foods until she finds what she is in the mood for, you know? Otherwise it will be donuts at every meal! The experts say that kids have to try new foods up to 6 times to decide if they really like it, so don't give up the first time she rejects something. Try it again on another day if it was a new food. If it is something you know she likes, then give it again the next time she sits in her chair. If she is hungry, she will eat. If she is not hungry, at this age it's okay to have them wait a while - they won't starve and nothing bad will happen if they are stubborn and wait a little too long. She can end her meal but you can stay at the table to finish yours. She can play in the other room, or sit at the table and play with a toy or a book, but she can't pull you away from the table before you are done. Either she will be happy doing her own thing, or she will figure out that all the fun is at the table with the family, and she'll want to come back. Either way, be consistent.
I agree about encouraging/reinforcing good behavior but I think it is important not to get into a battle. We cannot force our kids to eat, sleep or potty train - those things are totally within THEIR control. So we can only enforce proper behavior around these activities. If you can make mealtime fun with you and Daddy laughing and telling stories, maybe it will appeal to her. It will take time but you will be glad you did it.