The problem with handing it this way is that that he does know that this character was an issue and whats to stop from bringing another one that is not made using the rules. Granted this way makes no one unhappy and saves on potential drama for the moment but can just delay until further it down the line.
I'm presuming that this is the usual rough spot when a player is new to a group, and doesn't yet know how rules-tight they are.
As has been pointed out, his character is illegal, but not munchkin, nor even particularly overpowered. So I could easily see this being a case of him being a bit rules-ignorant, or having played in a game where they house-ruled things differently.
As I've mentioned a few times, I'm a rules guy, whether it's in my favor or not. House rules vary from group to group. Creative interpretations come and go. The written rules are the only source that everyone has equal access to. Additionally, as a DM, when someone disagrees with a ruling, I find it very convenient to be able to point to the rule in the book, in black and white, that supports my decision, and while I respect "Rule Zero", I try not to resort to it.
So I suspect that, once he knows the score for our group, he'll build something that fits in better. He seems like a good player. His character looks like it was built based on what someone else told him was cool or legit. I mean, I made the error, earlier in this thread, of confusing
Command Undead and
Control Undead. It's conceivable that he legitimately confused True Necromancer with Dread Necromancer. It's possible that he mistook "No Magic, No Master worked" for just "No Magic".
It's also possible that, in other campaigns he's played in, they didn't care about or enforce alignment restrictions.
I'm hoping that this is just a case of opening issue learning curve.