I'm not a professional English teacher, but I would say that both options can be correct in differing contexts.
"I agreed with her proposal" could be used without necessarily affecting the outcome of the proposal. It means that the speaker supported the one making the proposal or was in harmony with her.
"I agreed to her proposal", however, suggests that the speaker would act on or implement that proposal.
An example. Myself and two friends are discussing which movie to see. Friend Jane says "let's see Titanic" and I agree with her proposal. Friend Bob though, says no, and so we have to pick another movie.
If there were only Jane and I, and she proposed seeing "Titanic", I could agree to her proposal and we would then see that movie.
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