Better idea: Any and all alignment restrictions on classes, and limitations on spells based on personal alignment, can be waived if the DM rules that this is an exceptional case such that the reason for the restriction does not apply. Also, the alignment rules from BoED are thrown out, because they're totally absurd.

After all, just because a cleric of Pelor is able to justify things to himself doesn't mean Pelor is going to accept his justification. And a Lawful Good cleric of a LN deity might still be unwilling to channel evil energies even for the sake of good (if he would be willing, that's where my idea kicks in), and a Desecrate spell is going to be innately evil no matter who casts it. Malleable personality makes no sense at all; someone who has a certain set of values isn't going to change it even if they can (as then they might act in a way that would horrify who they used to be.)

A large part of "fixing" alignment is simply recognizing that alignment isn't a crunch concept; it's a fluff concept with a handful of crunch applications. As such, it's naturally subject to fluff-sort rules.