I'm pretty sure he knew he had to whack Pussy, I think it was more trying to justify it to himself. Tony seemed like that sort of guy, and he seemed to genuinely feel sad for Pussy, because he knew it had to be done. The whole interrogation scene was likely for his own benefit, so later on when he felt guilt he could remind himself "Guy was a fuckin' rat. You had to whack him or you'd be looking at 20-to-life right now in a cell" and things like that.

I don't think Pussy would have gotten a pass even if he hadn't given much information, because he still flipped. Also remember at this point, Tony already pardoned Pussy; they thought he was a rat beforehand, around when they whacked Jimmy Altieri (who it was never specifically explained if he was also a rat, just strongly implied). So Pussy already was forgiven, now Tony finds out he really IS a rat, and that spells curtains for Pussy.