Turn of phrase

There's a phrase that has long confused me, and when I came upon it last night in chapter 2 of The Amazing Adventures of Kavalier and Clay, I attempted to dissect it, and became even more confused than I was before. The phrase in question is "not unkindly". First of all, isn't that a double negative? Not + un? Secondly, it seems to be purposefully contradictory of itself. Let's break it down. First of all, the word kindly. Merriam Webster Online defines kindly as "of an agreeable or beneficial nature". So kindly = good. Moving on to unkindly, which is defined as "not kindly". Nice and succinct, there, MW. Unkindly = bad. Now, "not unkindly". Basically, what we're talking about here, at a very basic level, is not not kindly. It's so ...awkward. Why is it so often used?
The thing that really gets me, though, is how it's used in narrative. I think the reason it's so bloody confusing is that the context is never, ever clear. For example:

When the train at last crawled back into the Prague station early that evening, Josef remained in his seat, unable to move, until a passing conductor suggested, not unkindly, that the young gentleman had better get off.

That could so easily be taken either way. The conductor could be a nice guy and sympathetically tell the poor young man he needed to get off the train, OR he could just as easily be a total jerk and say "Beat it, ya bum." Obviously, given our new clarification of the phrase, the conductor is the former. But really, that double negative confuses us, and we're left unsettled, not entirely sure that we've read it right, and wondering if we're supposed to be feeling any more badly for poor Josef Kavalier than we already are.

Not, perhaps, the most enlightening blog post ever, but hey! Now that I've picked the whole thing apart, I understand it a lot more. And really, it's my blog. Isn't it all about me? I mean that not unkindly. ;)