2. Just to clarify, are you really saying that you would not eat at any restaurant in which EVERY dish and EVERY ingredient was kosher? This seems overboard to me. I certainly respect religious dietary customs (although honestly, I find some of them to be silly in the way that arbitrary rules from thousands of years ago are often silly), but this is a restaurant that clearly goes out of its way to be above-board about its ingredients. For instance, when they run out of their normal, organic chicken, there's always a sign informing you that they are using another chicken source temporarily, etc.
2) I do not keep kosher, however those who I know that do, do in fact do this. There are requirements kitchens have to fulfill to be kosher themselves. It's not my religion, don't expect me to explain or defend it.
3) I am suggesting that their signage was below par in this instance. I think they have resolved this well.
Perhaps they should simply offer the beans without the bacon in addition, but the half-dozen or so people I know that keep kosher would never eat at a restaurant that itself wasn't kosher or at least vegan. Is there a significant number of people who will not eat pork but also wouldn't mind if the establishment cooks with pork? I'm not sure how much of an issue this is in practice, I think it's kind of assumed here by people in the states that unless it says vegetarian/vegan/kosher, it's not vegetarian/vegan/kosher.