It's unusual "partir" in this kind of expression, the best will be use "irte" ... for me the expression will be: Si quieres irte, no suplicare que te quedes.
The expression is ok if translate it literally, word for word, what I try to said is latin spanish use more "irte" not "partir" in this type of expression. What ever I thing both options are ok.
I agree, a Spanish speaker would rather say "Si tienes ganas de marcharte, for instance. But there is nothing wrong with the partir verb, so I'm validating this translation. Besides, it's a "meaning only" request.