It probably wouldn't be the worst idea in the world. My only "concern" would be the incredibly, incredibly weird looks you're sure to get from co-workers. But....F'em. If that's all you can manage then it is, in fact, better than nothing. Just be sure not to slouch even though you're on the ball, I've seen people find ways to hunch over while doing shoulder presses on the ball. Fun stuff.
However, do you have a lunch break during the day? Would there be any chance to take a 10-minute walk around the block or something at lunch, before or after you eat? That's actually the first idea that came to mind in this situation.