As I said, the Feat would be enough to allow a Prohibited Spell IMC. I disallow Arcane Disciple for the exact reason Hypersmurf mentions it; the first thing that sprang to mind when I read it was: "Hey, Sorcerers can take the Healing domain. Gee. That's f'n broken." Wizards /=/ Healers. But I draw a big, fat line between Arcane & Divine magic. That's me. Thanee has a perfectly valid point: the rules can be interpreted as the spells are removed from the Specialist's list, but that's semantics and I haven't seen anything in the SRD that says that exactly. No touchy? That it says. But not that the spell no longer exists on the list. Again, semantics, and her point is totally valid, but now we're getting out of SRD territory and into HR territory.
Crossing the Divine/Arcane barrier? Zephyrus, it's your campaign, dude. If your friend just wants an argument, hey, let him make it. But it seems from here that you're pretty clear on your interpretation of the rule. If you want to allow Arcane Disciple, instead of getting just one prohibited spell, he can get a whole DOMAIN of spells. (Yeah, 9 spells, from a Cleric Domain, for the price of one feat. I say it's grossly unbalanced, but that's me).
So if you're just looking for a way to keep your rules adhering to RAW and canon as much as possible, that's the best (and most immediate) option.
LCpt. Thia Halmades