I have heard there is a mishna that talks about the negative conotations of a Bal Tshuva becoming an Orthodox Rabbi. Can you point me to this mishna if it exists?
There is no such Mishna. The Gemara and the Rambam discuss a Mamzer being a Rabbi. But as is obvious nowadays there is no problem whatsoever for a Ba'al Teshuva to be a Rabbi. Rabbi Yitzchak Grinblat