The distinction between "permission" and "ability" here is a little fine, I think. One way, after all, for a god to enforce a rule of prohibition on its clerics is to withhold a certain ability.
What you say about Flame Strike is controversial - it may be, after all, that Pelor would forbid such conduct, and therefore prevent the spell taking effect. Admittedly, such divine intervention in divine spell casting was emphasised in earlier additions of AD&D (I especially have in mind the 1st ed DMG) in a way that it is not in 3rd Ed, but you can hardly say that it is contrary to the rules of 3rd Ed for a DM to adjudicate divine spell casting in this fashion.
Sticking closer to rules literalism, the Flame Strike issue can be explained this way (as many posters above have done): the use of Flame Strike is not inherently evil, whereas (under the hypothesis I am exploring) the use of [Evil] spells is (either because of the powers they call upon, like Deathwatch and Summon spells, or the effects that they have, like Animate Dead and Contagion).
This does seem to leave some gaps - why is Energy Drain not [Evil]? - but (as I said above) no rules set is perfect.
The alternative interpretation, which divorces the concept of [Evil] from that of evil, likewise leaves gaps: it cannot explain why good clerics can't cast evil spells, and more generally leaves the relationship between morals and metaphysics, which is (and always has been) central to D&D, unexplained.
I'm not 100% sure that one or the other is the best way of going. The point I'm trying to make is that an interpretation of the rules which tries to maximise consistency with the text and minimise gaps and non sequiturs does not obviously favour your way of going against the alternative.