Buddy Rogers was the WWWF World Heavyweight Champion when Scooby-Doo, Where Are You! debuted on September 13, 1969. The series first aired that day on CBS, and the WWWF title at the time was still held by Rogers, who had been recognized as champion since the early 1960s.
That makes the answer straightforward: if you mean the original Scooby-Doo series debut, the champion was Buddy Rogers, not Bruno Sammartino or Pedro Morales. The WWWF World Heavyweight Championship itself was the predecessor to what later became the WWF and then WWE Championship, so the title name has changed over time, but the champion on that date was Rogers.
If you were asking about a different Scooby-Doo premiere, the answer would change. But for the 1969 debut of Scooby-Doo, Where Are You! , Buddy Rogers was the reigning WWWF World champion.