I was reading through the newest book again, and remembered this old club.
That inspired me to go through the books again, and I think I found a confirmation that Snape really did kill Albus on the orders *of* Albus.
In HBP, Elf Tails, Hagrid relates overhearing a conversation between Dumbledore and Snape, where Snape is saying "I won't do it!" and Dumbledore said "You have to."
Hagrid didn't hear what it was about other than that.
My theory is that this act, killing (or apparently killing, but I really do think he's dead) Dumbledore, is what that conversation was about.
Tie into that the later comment "Please, Severus" just before Snape commits the deed... it looks pretty clear to me now.
Of course, Harry won't accept that for a while (if ever), given his distrust of Snape, but that conflict will be a plot point in Book 7, I suspect.
Any thoughts?