Morality doesn't work the same for everybody. I prefer to look at how empathic the characters are but this also doesn't work the same for everybody, some people are only empathic towards their family for example. Some people are ready to sacrifice the things they have less empathy to for the things they value higher. You also need to look at the emotional state, personality (how pride somebody is) that could cloud judgment and disassociate one's values from oneself.
Walter seems to me (I'm only at season 3 right) to have a bit of mix of pride, really caring for his family and emotional issues. The emotional issues are probably because of the problems with his family and the choices he sometimes seems to regret. Emotional issues on themselves don't make somebody a criminal or make ignore personal values, the way somebody deal with this does (actually, could do). Walter makes an abstraction of the results the drug could have, he intellectualizes it.