A half-elf fighter who takes Thunderwave doesn't have the ability to use implements. He just doesn't. He's not "proficient", so to speak.
Similarly, a wizard who selects a fighter power for Dilletante isn't proficient with any weapons except dagger and staff, and has to use one of those.
These issues you mention are actually very different situations from each other. I agree with your first statement that a fighter doesn't have the ability to use an implement with his Thunderwave, as per RAW. But using the term 'proficient' to describe his ability or inability to do so is misleading. A weapon's proficiency bonus is not commensurate to the ability to wield an implement.
Anyone can use
any weapon. A proficiency, though, just gives the character a
proficiency bonus. Implements have no parallel to this proficiency bonus. You are either able to wield the implement or you can't; this ability is granted by one's class (or multiclass feat, or in the case of dilettante and many understanding DMs, DM permission).
If a half-elf Wizard used dilettante to get Cleave, he may not be proficient with the weapon he chooses to use, but if he's using a magic weapon, he still gets the
magic item enhancement bonus. A half-elf fighter with Thunderwave, if he can't use an implement, has
no opportunity to gain a magic item enhancement bonus because
he can't use any magic items with the power as per RAW (as we determined during your first point).
In summation, weapon proficiency bonuses are completely irrelevant to this discussion. It's the issue of magic item enhancement bonuses that we're concerned with, although weapon proficiencies can be confusing so I understand the mix-up.
~ fissionessence