No: Baseball was never pure in the first place.
Out of any sport, it seems that baseball fans are the ones who suffer the most from selective memory syndrome. Yes, the PED scandal is a disheartening blow to purists of the sport, but have you forgotten the amphetamines-era of the 1970s? Players were so hyped up on greenies that stolen base totals reached an unprecedented peak from 1971-1980. Increased alterness and adrenaline also contributed to the marathon throwing sessions that many pitchers took part in during that time. And that's only one instance on the long list of scandals in MLB.
The Black Sox, Pete Rose, Dock Ellis and his LSD-fueled no-hitter: baseball has been anything but clean nearly since its beginning. With PEDs, the circumstances may have changed, but the game is still the same.