Freezing doesn't kill microbes, at least not usually, it does tend to prevent their growth though. It's why you have to thoroughly cook frozen food and then let it cool back down, you can't just heat it up to the temperature you want.

However, ******ing microbial growth is usually enough. I store my bottles empty and open, and they don't go funky. Camelback's can be tricky to get air flow in, so I usually just roll them up and stick them in the freezer.