If he believed Charles was a zombie there would have been no reason to lie about what happened.
He knew it was a set-up, he knew Charles needed his phone so that he could take JJ to school, he knew Lori was not scared of Charles because she was leading the dance with the phone (and probably his car key too) and provoking the situation, not giving it back or acting like a scared person would, and he did not leave Charles alone with Lori to get his gun from the bedroom, because Charles would have left the house knowing he was being set up. He'd already been in text with Adam that Alex was there and they were setting something up. There would have been none of the chasing and tackling him from behind and grappling on the floor waiting for Tylee to leave, he would have been already armed for the protection of everyone, he would have said Lori had asked him to stay because she was frightened of him, not because they were planning a fun day out, and as soon as Charles got threatening he shot him. He knew it was an absolute farce that Lori would invite Charles to take JJ to school, if he was a zombie there to kill Lori.
He knew Lori had moved to Texas to live with "Hiplos", the worst and most dangerous zombie of all, and hadn't been in any danger. He participated in killing defenseless children, his niece and nephew, who weren't a physical threat to anyone. Why did he write too many kids, revealing Lori's problem, if he thought they were evil, and why was he casual and smiling in a photo with Tylee and JJ at Yellowstone, taking them on a day trip, if he believed they were 'devils'? This was all about being a remorseless killer, for hire. He knew exactly what the situation was as soon as Lori and Chad left, even though he'd had their blessing, been cleansed, and there would be no reason for him to hide from the circle, and his wife, what they had done, or think he was in deep doo-doo, if he truly believed. A fall-guy, one who hides what he has done from other believers, has cognizance and was not a true believer, he always had the capacity for pause, and for doubt. IMO