All are possible, except for one.
"They didn't agree John's plan" seems to be missing a word. You agree to, agree with or agree about something.
"They didn't agree with John's plan." John's plan was given as an option, and rejected.
"They didn't agree to John's plan." John seems to be the leader here and he went ahead with his plan anyway, despite what they thought.
"They didn't agree about John's plan." They had different opinions regarding John's plan. John wasn't there, apparently.