As far as I know, Susan McIntyre is the only licensed therapist offering gender counseling in Iowa. I wasn't aware she was using a church as an office, but she shouldn't have used their letterhead stationery. Her counseling was not a service of the church and use of its stationery suggests that her services were somehow affiliated with it.
So I guess she set herself up for this situation. Although I don't think she should have been fired from her housekeeping position, I guess I can understand the argument that she put the church at a legal liability and was thus an undesirable employee. But I suspect she was fired because she was suddenly controversial and the bishop feared her continued employment would create what the Catholic Church calls "scandal."
But I would like to take issue with what the article claims is a 2000 year old teaching on transsexualism. I don't believe there is any formal teaching about this topic, although parts of other documents have been interpreted to cover it.
Edit:
A closer reading of the article suggests that the letterhead did not belong to the church, although it did use the student center's name and address.
Edit Again:
Susan McIntyre has posted, in a comment thread, that she printed the letterhead on her own computer. She also states her intention to go to court.
http://www.bilerico.com/2010/01/iowa_catholic_church_fires_woman_over_transgender.php#comments