The various prophetic references are just that: prophecies. God is saying that if the people don't live right, they will be weakened as a nation and calamities will come upon them, including invasion by foreign nations that will do horrible things to them. God isn't saying that it's good or that it's right, simply that that is what will end up happening.

As for some of the other passages:

Forcing a man who has raped a woman to marry her doesn't sound like it makes much sense in a modern context, but keep in mind that this wasn't written for our civilization. He would be required to marry the victim and maintain her and provide for her and their children for the rest of his life, without being allowed to divorce her. Also, their culture placed a lot of importance on the ownership of land. When you lived somewhere, on your family's land, you tended to stay there, which meant you'd most likely be stuck living in the same place, around a bunch of people who knew the circumstances of your rather sudden marriage. All in all, it provides a pretty strong disincentive to commit rape.

One of the more interesting listings from the linked site:

5) Death to the Rape Victim (Deuteronomy 22:23-24 NAB) If within the city a man comes upon a maiden who is betrothed, and has relations with her, you shall bring them both out of the gate of the city and there stone them to death: the girl because she did not cry out for help though she was in the city, and the man because he violated his neighbors wife. It is clear that God doesn't give a damn about the rape victim. He is only concerned about the violation of another mans "property".

Actually, this is completely wrong. This law exists to protect everyone involved, and it actually demonstrates a rather impressive knowledge of human behavior and human nature. The key words here are "because she did not cry out for help though she was in the city," under the assumption that if she went along with it willingly, it wasn't actually rape. First, it protects the man from false accusations--if a malicious woman makes an accusation like that, she's on the hook too. And second, it protects the woman. If she knows that if she plays along, she's guilty under the law, then he can't use the best-known of intimidation tactics employed by rapists, "play along or I'll kill you!" It gives her a strong incentive to struggle, fight him off, and scream for help, which makes it less likely that she will actually end up being raped. All in all, this demonstrates the brilliance of God's law, not the cruelty and immorality of it.