I believe remaining silent in situations like this reinforces the negative at the expense of the positive - and that it does so in one way that gets overlooked by almost everyone:
With many people who are Christian, if they respect you but don't know your religious affiliation, they will assume (because they respect you) that you are "like them". At the very least, they will believe you aren't part of a "damnable cult" like Mormonism, as they see it. Your silence reinforces that stereotype and actually contributes to the solidification of their characterization - since they will look at you as an example of someone who knows better than to associate with people who are damned to Hell, like Mormons and Jehovah's Witnesses (and, in some cases and places, Catholics).
I believe there certainly are times when it's appropriate to remain silent in the presence of someone who is railing against the Church, but the effect described above is worth considering, in my opinion - no matter how you choose to act.