As I have said he is a Cleric of Pelor because he wants to be a Cleric and he is Human so unless he changes it he is a Cleric of Pelor, I have asked him about going a Cleric of Wee Jas and he is looking at it.
Maybe you are just going on the simple PH descriptions, but Pelor isn't exactly the "default" deity for humans. The deities in the PH are just a small sampling of gods from the Greyhawk campaign setting and a number of them are from human pantheons. Heironeous and Hextor, for example, come from the Oeridian pantheon, Oeridians being a subrace of humans in the Greyhawk setting. Wee Jas is a member of the Suel pantheon, which tends to be very humanocentric, even human supremacist. Vecna was once a human (then a lich) himself before he became a god. The only gods in the PH who are associated closely with non-human races are Corellon Larethian, Ehlonna (who has more an equal-opportunity goddess for both humans and elves), Erythnul, Garl Glittergold, Gruumsh, Moradin, and Yondalla. The rest come from pantheons that are human in origin.
I know the player well, he isn't demanding that he can do it in a way to power up his character, he is wondering if his character would be able to use his power to command the undead (until the end of the encounter) to attack the Necromancer and then they become...unraised? basically they go back to being dead. Since he can't command the Undead specifically he just gives the one order, one time (per casting but each undead affected successfully/unsuccessfully is immune to further attempts) to attack the guy who raised them, then it isn't too powerful, I think (that's kinda what I was asking)
No, the rules don't allow it. So if you are asking what the Rules As Written (RAW) say, no, he can't be a cleric of Pelor and have any ability to command undead. Whether or not you feel it is appropriate is completely up to you as a DM decision. But it really doesn't fit the character of Pelor or any good cleric for that matter to command the undead for any purpose whatsoever. The best favor a good cleric can do for the undead is to put them to rest. Deal with the necromancer after his minions are gone (which means he is probably much less of a threat anyway).
As was mentioned on page 1 it is a very situational ability and I was just curious if he would be able to be a Cleric (under any god) so long as he isn't evil, that could cast Cure spells, turn undead and on occasion where it is applicable command some undead to attack the guy who raised them (and the mechanics behind the ability)
There are no rules for this. You'd be going off the rulebooks if you want to allow that. That's fine, but you'd have to figure out what was acceptable and how to do it because its your game and it would be your house rule.
whether he is a cleric of Pelor is another matter (Pelor may allow the dead to get their revenge before they Rest in Peace) but if another deity would be better then I will tell him that
Pelor would not allow the dead to get their revenge because the dead wouldn't see it that way. As stated above, the best favor a good cleric (and Pelor for that matter) can do for the undead is to put them to rest. Using them to attack a necromancer is a slippery moral slope that probably shouldn't be tread upon.
Here is an interesting idea though, if you want to grab it. Perhaps the cleric uses a turn undead ability with the intent of controlling the undead to turn them against their master. From the cleric's point of view he is committing a small evil for the greater good. And for some reason, even though he knows it shouldn't be possible, it works. The undead fall under his command and attack the necromancer. Afterward, they fall over, their spirits released. The cleric thinks "Interesting, I suppose Pelor approves." But in fact, Pelor does NOT approve. The cleric, without realizing it, channeled the power of Nerull, who saw fit to grant the cleric with this power solely to tempt him to use it again. Eventually, Nerull hopes the cleric will grow to rely on this ability, even abuse it. At that point, Pelor stops granting divine abilities to the cleric and the cleric is forced to atone. But that is when the priest of Nerull steps forward and says to the cleric "Ah, but there is another way..."