when the user presses submit you could set a field e.g. my:formLock to a value, e.g. true.
Then in your rules which populate from sharepoint, add a condition which says 'if formLock is not true'. This way the fields will only auto populare (or in your case, RE-populate) once the formLock value is set.
The email which is sent with the form will have formLock set and the auto fields will not change.