When in doubt, ask them what they want. And respect their wishes. I'm pretty sure this is the basic rule in life, and especially if you're going to be posting stuff about someone (especially someone living!) on the internet.
If you are linking to a birth record, and the gender is different there, make a note. If there are kids later on, and it's complicated because (say) both parents are female---ask what the people involved want you to do.