I see that in the Greyhawk campaign, the deity Pholtus of the blinding light is listed as Lawful Good, nowithstanding that there has been an inqusition against mages and clerics of other faiths going on for some time in the Pale, a country where Pholtus is the only deity allowed to be worshiped! Surely, Pholtus knows about this by now, and presumably approves, or else he'd have stopped it... given all this, should he still keep his Lawful Good alignment? I don't think so! There are, of course, other examples I could give (including the alleged good alignment of certain real-world deities), but let's stick with Pholtus as an example... Should he turn in his Lawful Good membership card and become Lawful Neutral (or even Lawful Evil)? What's Your opinion?
Dubious alignment assignments...
Phlotus remind´s me of godess Ezra of Ravenloft. She is LG too but she has several different church sects that teach her dogma in different ways: LG helps poor, LN and N are scholars and theologiests, while LE are inquisitors and witch hunters who preach that all wickedness should be punished.
So maybe there is same case with Phlotus: he is LG but his church orders have different moral wiev on his dogma.
Ezra is fine excample what happens when god have little influence in lives of her worshipers.
Pholtus is lawful good with lawful neutral tendencies. According to On Hallowed Ground his realm, the Path of the Law, is in Mechanus. So he's more lawful neutral than even St. Cuthbert.
There's also a nation of lawful evil Pholtus worshipers, the Theocracy of Dimre, on Oerth in the Bandit Kingdoms. It was founded by followers of a paladin possessed by the Hand and Eye of Vecna, so perhaps it's really Vecna that grants them their spells.
The Pale is firmly lawful neutral in alignment, and Pholtus approves of them just as much as he approves of his lawful good followers. He's probably closer to the lawful neutral ones, though.
According to Greyhawk Adventures, Pholtus is Lawful Good (Lawful neutral tendencies), his followers can be LG, LN, or LE, and his priests can only be Lawful Neutral. So draw your own conclusions from that.
I would summarize it as: "Pholtus is a deity who has good ideals himself, but believes that only rigid obedience to his Law is necessary in others. He sees his clerics as enforcers of his Law and does not permit sentimentality in them, and does not permit them to bend the law in the name of mercy. He believes his Law is perfectly constructed and will inevitably lead to Good, but only if it is followed to the absolute letter. He believes that only he can be trusted to know what is good; for others, their role is to simply obey, at least until all chaos is eliminated from the cosmos."
In looking at how alignments have been assigned to various real-world gods, and comparing that to the mythology about them, I find several of those alignments don't fit...
That is true. Greek mytholgy is full of that stuff: Greek gods have nasty tendecy to horibly punish those who they dislike (their most comon flaw is jelaousy), some of punishments are fit but other are litle too much: for example Apollo and Artemis have slaughtered 15 sons and 15 daughters of Medea just becaouse she said she is better mother, and Ra (who said that humans are his children and no harm should fall on them) ordered godess Sekhmet to slaughter humans for some reason (but I forgot it).
But then again even good gods are entitled to some divine wrath sometimes, after all you need to show mortals who is the boss or they will get some crazy ideas in they head and you will find yourself floating in Astral. 
If I recall correctly, Ra was ticked off because people were scoffing at his power, and some were even suggesting he didn't exist... and yeah, the powers of the "pagan" pantheons commited atrocities from time to time too, just like the One God of monotheism... the main difference is the motivations for doing it (pagan deities usually don't get mad at people for worshiping other deities, for instance), and the fact that with a pantheon not all the gods agree on the rightness of the actions of one of their number (whereas the angels of monotheism never seem to disagree with the One God, or if they do they don't say so or act on it... with the notable exception of Satan!)
To hold against vileness sometimes you must use a wall of violence, but the true atrocity would be not to build that wall and let that vileness unleash on innocent people. Had not that church fought for its rights, it would have fallen under the mauls of the heretics many years ago. Anyway i'm quite a fan of subjective alignement, as i think it can be a challenge to the devoted PCs. An example is an old adventure based on the last days of Costaninoples: both the leaders of the war considered themselves good and pious (and were rated as goods in their stats) but they fought each other also for the sake of faith. I think in many game worlds one or more strong churches could be very characterful, and maybe can help going beyond the do ut des of "i worship my god/i get my spells and special abilities". This would be quite difficult to use on a Planescape setting, where gods are not very trascendent.
It all depends whether you want to run your game with a subjective or objective view of the alignment system.
This would affect things like a Paladin's Smite Good ability working on another Paladin who serves an "opposing" deity. They may consider themselves to be lawful good but their enemy would consider them to be corrupt and evil.
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