Nathan had already dropped the gun when the whispered request came. "We're not gonna kill you, Gabe." If anyone heard specific inflection on the diminutive, it was because it was intentional. All along, Nathan had been certain to draw a very thick line in the sand, thicker still when Gabriel had become closer to all of them, and they needed Gabriel to stay on the right side of that line.
His attention turned to Peter. Headache. You said he had a headache, you were looking for something for it just before this happened. What was the headache about? Is there something wrong with him?
A drastic change in personality. Removing the Sylar aspect, usually that indicated brain trauma. Perhaps something was wrong and it had effected the ability Gabriel had?
Nathan was trying to explore all options, to give all explanations a fair shake, as he didn't want to think Gabriel had just gone too far, that Claire's concern over what Gabriel had expressed to her was the last of what was truly Gabriel.