Good question, dt! Technically, Clemenza was liable, since Paulie was his guy. And as you noted, it was Clemenza's responsibility to whack Paulie (at least partly a loyalty test), and as Threlkis said, Sonny definitely could not dismiss Clemenza as complicit until he got the phone company records.
But, the bottom line was: the family was at war, and Clemenza was needed. Technically, hothead Sonny could have demanded that Clemenza fall on his sword (or stabbed him with the sword), but he needed Clemenza for the war.