"Whether Mary's adoptive parents were homosexual or not does not matter; THERE ARE NOT HER BIOLOGICAL PARENTS. You can trace Joe and Henry, if you want to, but their ancestors are not Mary's ancestors."
... and I think you have come to the point of the original poster's question. Let's say Mary's biological parents weren't ever married. How would you enter them into FTM or Ancestry.com? No matter what you do, they are listed as each other's spouses. It's misleading.
And ultimately, the information you determine is essential depends greatly on whether you are related to Joe, Henry, or Mary. In my opinion, every familial relationship ought to at least be acknowledged.
Regarding same-sex and other relationships:
FTM 2011 will allow you to enter same-sex couples, but again you only have the option to be a "husband" or "wife" (and "mother" and "father"), not "partner." It will change the status to husband or wife (based upon the gender). For example, I entered two females and they were both listed as "wife."
I know that there is a family tree program out there that allows non-traditional relationships such as "partner" ... I just can't remember whether it's RootsMagic 4 or the most recent version of Legacy.