This may seem controversial, but I think there should be an option to list a gender as 'unknown due to miscarriage'. As a mother who experienced miscarriage a few years ago, I do hope that the baby I lost is a member of my eternal family. I don't know if that is the case, but I do know that it is document-able-- there was a date of diagnosis. Many of these children have names, and for some of the children the gender is evident.
Even if this idea is not implemented, I hope that familysearch-- and in extension, the church of Jesus Christ-- will seek guidance regarding this issue.