The thing is, Fraction's tendency to bizarro pacing made Pepper's Tony-blaming look like a much bigger deal than it actually is. Fractions spun it out over several issues, but all those scenes together add up to a single fairly short-term freakout that she had as a reaction to finding out that Tony had a plan to come back all along. There's no indication that she'd been dwelling on Happy's death and holding Tony responsible ever since he pulled the plug, and there isn't even any indication that she's dwelling on it now, post-surgery. I'd be pretty suprised if she brings it up again.