If I can hazard a theory, I'd say that the writers want some moral ambiguity, but not as much as they've created.

At least the way I read it the 2nd half of S2 tries hard to redeem Uther and Gaius, after previously having set them up as oppressors, and makes "Team Evil" more evil (with the Morgana Passivity Exception Clause). It's not entirely working, but I do think they are trying.