Me and one of my best friends started doing 5x5 workouts back in late 2008. He has a bad back just from bad genetic luck, but we took our time getting in to this routine and made sure we used good form and so on from day 1. We ran it together for the better part of a year, and his back problems disappeared. Life goes on, and we both quit going (I haven't posted here for over two years myself). He wasn't out of the gym six weeks before he threw his back out for the first time since before we were working out. He followed the Bill Starr rehab routine for the back (it's around on the net), and now he is fine.
This is all a very long way of saying that I really believe, and have some anecdotal evidence to back me up, that following a 5x5, that starting conservatively, sticking to your initial plan, being sure to develop and use good form always, and being patient will actually make a lot of bad joints feel much better as the bone, ligaments, tendons, and muscle become stronger and you become more flexible. I wish I had never quit going, not because I have a ways to go to get as strong as I was again, but because overall I just felt much better.