Where does this leave the Bible?
The fact that the Bible is mostly silent concerning intersex does nothing to discredit the text nor its source.
It wasn't an issue in ancient times (which doesn't mean it never occurred) that warranted special attention. Modern statistics posit that 1 in 1,666 births have some form of hermaphrodism. In ancient times, infant mortality was perhaps as high as 30%. The quantity of people with this trait would likely have been fairly low, especially among all but large cities. Physical deformity was commonplace enough (disease, warfare, etc.), so it stands to reason that even people with intersex traits would have been seen no worse than someone with some other physical defect.
Nothing written in the Bible guarantees everyone the same chances in life, including the chance to marry. Sexual intercourse is ordained by God for all people (Ge 2:24), but only within the confines of marriage. Poor people, people with awful parents, people who contract crippling illnesses, and the like are essentially in the same category with respect to the question of why doesn't everyone have the same chances in life.
Sex and sexuality were never meant to be the defining characteristics of an individual. Modern societies have made it such an issue that people want to define themselves according to their sexual desires, but this is not an important classification in Christianity.
Christians believe that God loves all people, and has placed them in their particular circumstances for his own reasons, none of which include callousness or cruelty. Every human being (except one) has sinned, and are thus fallen, broken creatures in need of a savior. In this sense, we are all equally at a disadvantage, because nobody can save himself.
Consider James 2:5 (NASB): "…did not God choose the poor of this world to be rich in faith…?" Those that we think of as being disadvantaged are not worse in every way. Similarly, those we consider to be extremely privileged do not always have it easy when it comes to important things, like putting their trust in God instead of wealth (e.g. Mt 19:23).
God has called all people, in every situation, to himself, and he commands that we love them all, just like he does. This is the hallmark of Christianity: that "you have love for one another." (Jn 13:35, NASB)