Why is doping illegal in Tour de France? It seems like a self-evident truth, but I've never heard the rationale behind it. Why is doping illegal in Tour de France?

I assume it is related to the safety of the riders? Then why don't they simply limit the doping to forms of doping and medical treatments that have been peer reviewed and demonstrated to be relatively safe?

Yeah, sure, it can never be completely safe, but that can be said for the sport itself, and any other sport. Riders make contact in Tour de France, they fall, there are inherent hazards to the sport. This is true for almost any sport.
You have to draw the line somewhere. If you allow all doping, then the winner will be the one most willing to sacrifice their long-term health to use the most drugs and maximise performance enhancement. 


  Then why don't they simply limit the doping to forms of doping and medical treatments that have been peer reviewed and demonstrated to be relatively safe?


They do this to a certain extent. One of the three criteria for adding a drug to the banned list is that it represents a health risk to athletes. There are also some substances which are allowed up to a certain threshold. Asthmatics (and non-asthmatics if they feel like it) for example are allowed to use a salbutamol (ventolin) puffer, but if an unreasonable amount of salbutamol is detected, then it is deemed as being a performance enhancer instead of being used for health.

The two other criteria for banning a drug are about fairness. They are "If the substance is performance enhancing" and "If the substance violates the spirit of the sport". If a substance meets two of those three criteria, it can be added to the WADA list of banned substances. You can read more about this here.