I think its actually very important for childrens` literature to show less perfect relationships. My DC love Harry Potter, but all commented on the unhealthy relationship between Hermione and Ron and said there is no way they would want a relationship like that.
To be fair, Lily and James Potter don`t seem to have had the healthiest relationship either, nor Remus and Dora, though for different reasons.
My DD is now reading Stephanie Meyer`s Twilight series, that is just one big bag of bad romance, but its been brilliant to open up a dialogue and discuss with her what is wrong with the relationships it portrays, what the red flags are, what the characters could have done differently and so on.
Historically childrens` stories were always intended to pass on messages and be cautionary, not just entertaining, I would say its a positive thing if they can still be used in such a way.