I guess it's kind of an interesting thought experience to consider what would have happened if no one cheated. Would Bolt still be the fastest man if everyone had to compete with their natural abilities? I would assume that he would at least still be among the fastest. But the unknowable question is whether everyone is getting more or less the same benefit from the PEDs and the doping, or whether Bolt got a bigger boost from those things.
At any rate, we'll never know because everyone at the top of the sprinting (and cycling, etc.) world is doing something against the rules to maximize their competitive advantage. You cannot reach the top if you are keeping the rules. The high end sports are a display of what dedication, focused training, the best talent, and also the latest science can achieve.