It does mess with the teeth. My son's living proof with a large gap between his top and bottom teeth only evident in the front. Since we've stopped giving him the paci so much, it's starting to go away.
It can also mess with speech development. I hear it every week from our speech therapist about getting rid of it completely and we're workign on it. They can't form the words right or use their tongue properly if there's a huge piece of rubber blocking the way.
Sam's almost three and only takes it at night and at nap at home (doesn't get it at the sitter's for nap).
I'm a huge proponent of paci's over thumbs, but having a delayed child, I can definitely see where taking it away earlier rather than later is MUC BETTER.
My sister had her daughter throw them away as she bit wholes in them. once the last one was gone, she was over it.
I know lots of people who "mail" the binkies to Santa or binky fairy for the new babies and get a prize in return (Santa/fairy is a relative).
She's soothing herself.....only you know how best to do that. Maybe start talking it up and include a conversation abotu trading "up" to a big girl soother, like a doll or special blanket.