Not sure it can be fixed. Like it or not, pro cycling is a lab for sports around the world. What do I mean? The stuff that ends up in pro sport (baseball, football, etc) was tested in cycling and running. Here is why:
#1 You can see if something works. Extreme endurance sports will simply test the key aspects of a PED. Can it make you strong, go longer or recover faster?
#2 These sports are rigorously tested. That is bad for those that fail, but it is good for the makers of these drugs and for athletes in other sports. They can find out what can be found by what tests.
#3 You have an endless supply of lab rats. This is key. History has taught us that riders and runners will not stop taking these just because they might get caught. Every year people get caught. They are willing to risk trouble and health risks for glory. That will never go way.
As JP said above me - drugs and sports are not going to split. People have been willing to do whatever it takes to get an edge since sports started. Those who say 'baseball players or cyclists back in XXXX years did it the right way' and that is total BS. They never had the choice of PED's. Many would have taken them to be the best. Athletes used to shot up with pain meds to fight through injury . . . that is the same damn thing in the big picture. Using science to allow them to perform when they would not, even if it hurt them later in life. The best have always looked for an edge. It is just that there are illegal edges now. When they figured out that protein helped build and repair muscles, athletes drank eggs. When gatorade testing proved what electrolyte replacement in a carb beverage could do, every athlete started to use it. These are not illegal, but they can improve performance.
The idea of two tours is dumb. Why? People will cheat to win the non-cheat version - that would have the most glory. That is essentially an honor system which is clearly not working these days.