I am not totally sure what the Montessori philosphy is. But, to me, I think it is a bit extreme for time out for not listening after only one time. What out about 1-2-3 methods? To me, I think is actually more useful to the child to give her several chances to modify her behavior on her own before she is placed in a time out - thus the 1-2-3, THEN time out, with plenty of warnings that she may get a time out if she does not change the unwanted behavior. This helps the child develop an awareness of what she is doing and what will happen if she does not stop. Can you even be reassured that when your kid gets a time out after one mishap, she even knows why she is getting time out? I mean, think about it...if you are told at work, don't use that red pen. OK, you try not to use it, but you need write a quick note and you grab the pen, perhaps not even aware that you did it, and out of nowhere your boss "time outs" you by banishing you to a corner of the office for 20 minutes. You'd be like, well, that's not fair! I should have at least been warned, I would have jsut dropped the pen. A time out out with very little or no warning feels like punishment, just for punishment's sake, not so much for learning sake. And what about redirection - distracting the child into doing a positive or safe behavior and then the unwanted behavior can stop. Simple, effective, and the child does not feel punished.
Sure, I agree that many 3 year olds can be "trained," or whatever, to learn good behaviors when only told once...but at the same time, they are just babies! Developmentally they are still so young, and everything is so new to them - from potty, to dressing themselves, even language is not fully established. Many, if not most, are still not developmentally able to control their impulses. It is not totally their fault they are not following directions. Cut the kid some slack. In fact, I would think that a time out for not listening the first time would result in an awful lot of time outs...first, the efficacy of the time out is reduced as the child is "desensitized" to it, second, the child may develop poor self esteem if she feels she is always getting in trouble.
I say, if you are not comfortable with this (and I am with you, I would not feel comfortable either) - definitely state this to the school. If they are adamant about following this form of discipline, then I would strongly consider changing schools.