It seems to me that this could be one of those passages that could easily be twisted to mean something completely different from Paul's original intent. After all, the passage repeats again and again that people must not judge on another—so by that definition, then pretty much anything is fair game, right?
If this passage could be used to justify pretty much anything we do—if we say, “Don’t judge me just because I lie and keep secrets, because I’m doing it so that others don’t get hurt”—well, it only takes a few more steps to get to justifying the Crusades and killing innocents, as long as it’s being done “for God”. This passage is not supposed to use to justify our actions or our misdeeds as long as they’re dedicated to God. The point is to recognize that we all make mistakes and we all sin, so there’s no point in being judgmental because then we’d all be pretty darn judged (and found guilty) anyway.
Of course, there are more subtle judgment calls, such as disagreements over theology— like the nature of God, or what is a sin and what is not. There are some things we can all concretely agree are sins—like idol worshipping or adultery, for example. But what about those things that sometimes fall in the gray areas? For example, a friend of mine and I used to argue about whether killing was actually a sin—we agreed that murdering was, but what about killing someone in self-defense, or in order to save the lives of others? Would killing another in order to save loved ones be a sin? One of us has to be wrong, of course; killing can’t both be a sin and not be a sin simultaneously. However, we both recognize that though one of us is wrong, that doesn’t mean that either of us is going to Hell or any such thing simply for being wrong. We’re just trying to follow God as best as we know how, and try to discern His will as best as we know how (spending time praying and carefully reading Scripture helps the most with this). This is what Paul means when he writes about no matter we do, we must always take care to do it in honor of the Lord. Don’t stress about technicalities, being judged, or always knowing the proper way to act or even the proper way to think; the most important thing is that we act sincerely and earnestly in order to glorify God with our actions. As long as what we do comes from the heart, through careful time spent with God and His Word, then we will truly be honoring Him.