The fact that the pope met with these people is not significant in itself - as you are obliquely pointing out, Christ spent most of His time with sinners. But the consistent message Christ delivered was that sinners should forsake their sin - not that society should accept their sin as normal.
So what will be more interesting will be what message comes out from Francis about the lifestyle this woman has chosen - does he think it should be accepted and embraced, or does he call for those in these cases to come to repentance and a change of their path?
How would a surgeried transexual do repentance? Dress as a woman?