If you're legally allowed (and you aren't intentionally fudging the numbers) then I don't see how paying no more than you actually owe is wrong. Now, if you know for a fact that a certain loophole is just that, a loophole that wasn't meant to be and will soon be fixed, then maybe you could make an argument that you shouldn't take advantage of our government's stupidity. But even that's a bit iffy, and most of the time, that's not the case -- they knew what they were doing. Even if the deduction is stupid, I don't see how you deciding to nobly sacrifice some of your money to not take advantage of it helps anything.
Maybe not morally reprehensible, but it's kinda stupid. But I mean, if you want to go on some pointless little crusade to reduce the national deficit by .000000000001% by not taking advantage of that deduction, and that'll make you feel good, then by all means.