I just came up with what I think is a good explanation of a compromise, although this may not be the case, since I'm running on four hours sleep, and that was a long long time ago.
Anyways, I tend to agree with some of the arguments that grave-robbing from tombs of the "innocent" is not virtuous. It's like stealing from the rich and keeping it for yourself. Sure, the rich may not've been using it, but that doesn't mean it belongs to anyone who has the means to take it.
But Virtue works on a relatively large-scale... uh, scale. A petty pickpocket might be TN. He steals stuff for a living, so his virtue should, theoretically, drop continuously, making him NE. He doesn't murder people or anything, doesn't beat his wife, doesn't do any truly abominable stuff, but he's still a thief. I don't see people thinking he's as diabolical as Irenicus because he steals stuff.
On the other hand, if a Paladin steals something in such a manner, he'd fall, yeah? A priest of Lathander would probably lose his granted powers, too. Huh. Okay, my idea has morphed from what it originally was (thievery incurs no virtue penalties, because it's not large-scale enough to be warranted), to something entirely different: Certain virtue hits only drop you into the "neutral" scale of things. If you steal something and are good aligned, you take a virtue hit. Once you've fallen to neutral, you only lose virtue by doing truly nasty things, like murder, rape, and graffiti.
Sounds like a lot of work for very little gain, though. First of all I'm not sure how Virtue's implemented, exactly, so I don't know how hard it'd be to add separate types of crimes, and second of all, I forget what's second, and now the weariness has kicked in and I'm fading fast.