The only reason I kept it at all, really, was because there are game mechanics that use it. What good is Detect Evil if you never define what Evil is?
And I agree with what you're saying. My gods tended to be more complicated than simply being Lawful Good.
For instance, one of the major gods that my games dealt with was Avos, the Lomonthian god of the Sun, War, and Men. Technically, he was Neutral Good, but obviously it got a lot more complicated than that. His paladins were part of his War Aspect, and thus had rules that specifically dealt with war. His priests dealt more with Fire and his attributes as the 'Perfect Man', so they handled issues like the proper duties of a Husband, Father, Son, Brother, etc.
I can stick him in a bucket, but the bucket was hardly a perfect reflection of what the religion viewed him as. In fact, his Paladins specifically split away from the aspects of Family by not having any of their own. If you looked at their vows and views, they aligned more with Lawful Neutral than Neutral Good, even though that's not the Alignment you'd give the god.
Ultimately, I used alignment as a rough guideline and something to help new players. My veteran players rarely concerned themselves with alignment beyond what mattered for specific game mechanics. New players, though, I find really need something to latch on to and an Alignment gives them something to use to help define their character. I never, though, restrict them from doing something just because of their alignment. I will, though, use the alignment they picked as a way to help them define and refine their character. Saying "You have your character listed as Neutral Good, but this action goes against that. Is this really what you want them to do? Why? What makes it ok for them to do that?" is a good tool to help someone develop their character and even stay in character. If they still want to do the evil action, maybe they have a good reason. Or maybe the character's alignment is shifting over time. Both of which are fine and can make for great roleplaying moments.
It's not a bad system, really, but like you said it's 'role-playing training wheels'. Useful when you start, but eventually they just get in the way.