That episode you are not supposed to take the trans person as an example of an actual transsexual.
If you watch the show throughout the seasons, Mr. Garrison is well known for being ignorant and racist, and indecisive of his own identity. First he wants mexicans out of south park, then he is homosexual, then he wants a nose job, then he is a transexual, then he is an extremist christian, then he is a violent atheist, then he is a man again.
Mr. Garrison is the manifestation of discrimination and ignorance. He is to be learned from his actions, and not his preaching. South Park is saying DONT BE THIS PERSON! They are not saying THIS PERSON IS CORRECT!
Also, that last line in the episode was priceless! "Well get an aids test thomson cuz your wife's a dude, ->-bleeped-<-got!"