Greetings,
This is a philosophical question as well as a practical one.
See, a lot of people will give culture more weight than it ought: making it trump the commands of Scripture when weighing the morality of a standard.
Some people, however, will do the exact opposite... in a way. They will reject a culture because the beliefs of the people who created the culture are contrary to their own.
Both people are really doing the same thing: they are equating culture with doctrine. The one group says their culture is the same as their doctrine, so throw them both out; the other group says their culture is the foundation for their doctrine.
Both are wrong.
See, doctrine deals in right and wrong. Culture deals in preferences. Like personality preferences versus character skills. Introversion is an example of one, and honesty is an example of the other. Having a 'preference' for dishonesty merely means you have a temptation to lie. Having a preference for extroversion merely means you have a gift that God gave you... and vice versa: having a preference for introversion also means you have a gift that God gave you.
Doctrine can say, for example, that stealing is wrong. Culture, on the other hand, can say that pink shirts are only worn by children (of either sex), and not by adults.
Or...
Doctrine can say that it is wrong for a girl to have short hair. While culture says girls should have short hair.
They can be compatible (like in the first example there), or incompatible (like in the second). When they clash, we go with doctrine, of course. Or we should. (Making sure, of course, that they really do conflict and that you are sure of both.)
Now, in our books, we have cultures. Tons of cultures. Or we should.
And we often have the tendency to have the 'badguy' cultures all conflict with our own doctrines (and preferences), and have all the 'goodguy' cultures all coincide with our own doctrines (and preferences). But this isn't accurate... or good storytelling. Or good teaching for that matter.Because that is the single best way you can possibly have to preach at people, without saying a word. Even if you don't say pink should only be worn by girls, if you make it so that the elves in your world (who happen to be right about everything) only let girls wear pink... then your readers will subliminally get the message that you believe only girls should wear pink. And if they happen to think differently (which a good many people do, and for good reason), they will feel 'preached at.' And that feeling will spill over and taint everything else in the book. They won't be able to enjoy the book as well, and they definitely won't be learning anything.
Does that mean you should reverse it? Make all the badguys have good culture? No!
It means you should make your cultures realistic, instead of flat. Even flat out wrong! Just because someone is wrong about something in your book, doesn't mean he needs to be corrected about it: pick your battles, and be realistic with the rest. You know you don't want to make your character just like yourself... so don't make your cultures just like yourself.
What are your thoughts on this? Have you lapsed into making your cultures flat by matching them to your own preferences? Do you have conflict between doctrine and culture in your stories?
In just our culture today a lot of doctrine and culture clashes, I think it would make a book more realistic to incorporate that into the book. 
In my Shapeshifter story, for example, the cultures of the Shapeshifters and humans are nearly perfect, but the Vandel's culture is absolutely horrible. *needs to work on that*