The stomach's pH is what does the most damage to the probiotics and affects their viability. They are very vulnerable until they reach the intestine - so I'd leave them in the capsule (if you're trying to heal the intestine). The viability issue is also why it's important to have as high a "count" of live organisma as possible, bc then you have the highest chance of more of them reaching the intestine alive (more likely).
THIS ARTICLE is probably more than you'll ever want to know, but I think the take away for you might be this:
"How you use a probiotic depends on why you are taking it. If the primary purpose for taking the probiotic is to aid digestion, then you must take it with meals. If the goal is to have the probiotic reach the lower intestinal tract, then it may be more appropriate to take it between meals, with a full glass of water. Water dilutes the stomach acids and moves the organisms quickly into the intestinal tract. Probiotics can also be used for both purposes by taking some with meals and some between meals. We suggest taking probiotics first thing in the morning and at bedtime, with water."