There's basically nothing you can do that isn't bad for some part of you. Living produces wear and tear on your body.
I switched to a primarily standing desk about three years ago and, anecdotally, it's been going great. I don't think I lost any significant amount of weight because of it, but my back doesn't get tired, and I generally feel less lethargic at the end of the day. I also feel like it helps my working because I can more easily pace around my office when I need to work through a tough problem.
Most people who recommend standing recommend alternating between standing and sitting every few hours, to avoid the kinds of issues you mention.
But I think part of it has to do with your general fitness level. If your legs are strong, your knees are in good shape, and you're not carrying around too much extra weight, you'll probably hold up a lot better to extended periods of standing. Then again, if you're not really in shape, you may have even more reason not to sit all day.
Personally, I sit while I eat my lunch, I typically sit a bit more on Mondays, and I just generally sit when I feel tired, but I spend most of my work day standing. And you don't need a fancy convertible desk, just a set of cinder blocks to elevate your desk, and a high chair to sit on when you feel like it (the kind you find in electronics labs).