I would never punish a dog for growling. This will just lead them to stop growling all together, which is a warning signal you want to be there. I would stop trying to be the 'dominant' one and start trying to be a team. You need to teach her she can trust you. (EDIT: I see you aren't worried about being the 'dominant' one. That's good :-D) She's uncomfortable with how close you are to her food because she thinks you're going to take it away. So in essence, taking the food away will just reinforce her behavior because you ARE taking it away. Instead, I would take a handful of kibble out of her bowl before you give it to her, sit next to her as close as she is comfortable, and casually toss a kibble in her bowl here and there. She will learn that you are the provider of good things, and when you are around, you give her things. If you ever do need to take her bowl away, it's best to trade it with something amazing, like a little bit of shredded boiled chicken, or something way higher in value than plain ol' kibble.
There are quit a few good books on resource guarding/fear issues.
This one is EXCELLENT
http://www.amazon.com/Mine-Practical.../dp/0970562942