The crossbow analogy makes sense, sure, and I have no problem with that.
The Flaming Sphere is a big ball of fire however. I can't even imagine 'directing it right into their weakest spot' when standing adjacent to the target, but perhaps I imagine the power differently than you do.
The Coup de Grace granted maximum damage would come, in my mind, not from hitting the weak spots specifically, but rather from the target not being able to protect their exposed flesh (weak spots) by shielding say, the face with your leather clad arm, or whatever.
It's not that I can't imagine how it would look if I thought the rule made sense in this case. It's just that I don't believe the rule was made with conjurations in mind (those rules don't seem to have been finalized when the PH dropped). Summonables, as creatures, can Coup de Grace, no?
The question that occurs to me now is; is it unbalanced to allow the conjuration to be able to Coup de Grace if they, and not the PC, are adjacent? A conjuration that can attack determines line of effect from the conjuration itself.... hmm...
Is it worthy of errata? Likely not...
Honestly, it's never come up in my game.... spell casting is noisy... but I'd Flaming Sphere Coup de Grace if the target didn't make it's perception check.