No, it's okay to take calcium and yogurt. One, the yogurt has calcium in it anyways, and can help on that level, as well as the probiotic level. Secondly, since this isn't a bile problem, you shouldn't have to stay on the yogurt and calcium forever anyways, so it really doesn't matter which one helps more. You may even find that the probiotics help your acid reflux. It all depends on if it's bile that you're refluxing or if there are bad bacteria in there (or just an imbalance) that's setting off your stomach acids. The last bout of trouble I had, after taking an antibiotic, gave me some heart burn. That's mostly gone away now, though. Of course, calcium can help cut the acid and the irritation caused by the acid in your stomach and esohpagus (yogurt being better for this so high up than the pill). My mother has always treated her reflux with milk. There's evidence now that the fat in the milk makes you make more acid, but I think her acid is bile, not stomach acid, and so that may be why she feels better than most people after having a glass of milk or a milkshake. At any rate, the yogurt should have enough benefits to squelch any extra acid it may (or may not) produce.
Try the yogurt once or twice a day and start out with one calcium pill a day and see what that does. If it doesn't do enough, up your calcium pill to two or three a day and get two yogurts a day. If you start getting constipated, cut out the calcium and just stick with one or two yogurts a day. Do that until you've been normal for three weeks, then go off everything and see what happens (if anything).