Interesting theory
Evidence FOR the Governor to be officially dead:
1. Everything that was shown in the show to that regard. By all accounts dude should be dead. 2. His listing among the casualties during The Talking Dead.
3. The fact that he also dies, killed by a different Lily, in the book during the assault on the prison.
4. Given the arc of the Governor on the show, it made sense for him to die then and there.
However, here are the loose ends that perhaps make a case AGAINST him dying:
1. We never really see his face/head getting blown off. This is not me being morbid or graphic, but considering we got everyone else's graphic deaths right on our faces throughout the episode (from Hershell, to the key players in the Governor's group), it's odd that we don't see the final fate of the Governor on screen. We do see a fallen chess piece, which could be a reference to his literal death or to a metaphorical fall of the leader of the group/family (but not his official death). Just saying, a character of this magnitude, you want to know that he's dead-dead. I don't believe in the Michonne approach of skewering the guy and giving him the look of "you so dead now", but not sticking around to see it through or finishing the job.
2. In the books, prior to the attack on the prison, he's maimed very badly by Michonne. As in missing-limbs badly. So the character has the potential to come back from pretty horrible stuff. Again, another case for sticking around to either finish the job or making sure the guy dies for realz, Michonne!
3. Interesting that David Morrissey was not invited to bid adieu to his character on the Talking Dead (as is customary). You have Hershell, and Kirkman (the writer and creator of the comic book), and... Maggie! WTF? Where is David Morrissey to talk about the last time we saw the Governor... unless... it's not the last time?
4. Although the arc makes perfect sense for the character, I'm wondering if it makes sense bringing Morrissey back for just 3 episodes (and a glimpse at the end of another) only to be killed. Granted, all three episodes really concentrated on him, but still...
5. And what about Lily? What is her fate now? Did she get killed? Did she run away? Does she have anything to live for? Or does she have another purpose in this story? I can see a scenario where she shoots close to the Governor's head, and then decides she's going to get out of there alive with this bastard. She may want answers before she really kills him, she may not have the killer bone in her yet, who knows? But I'm not sure of what would the show do with her at this point... except abandon the character into oblivion OR... use her as an excuse to get the Governor barely alive out of this one.
I know, too many what if's, but I do think the lack of a visual of an uncontested death of the Governor AND his absence as a guest in the Talking Dead are my biggest (and closest to most legitimate) red flags.