The biggest problem with legalising doping in professional sport is that it'd propogate down further into the amateur side... e.g. If Vino can do x then surley so can I do the same to win my clubs annual TT.
All sports are full of people cheating to gain an advantage - look at F1-gate, Crickets JellyBean-gate, Tevez-gate.
The full stage coverage of le tour means the only way to cheat is to take drugs, and this is well publicised. You don't hear so many calls for Tennis or Golf events to be called off due to drug taking, but it's still alleged to be prevalent in those sports.
There's no simple solution, the bad publicity will have to be lived with until the sport is clean and the media gaze moves elsewhere. Although the nature of the TdF and the coverage it gets draw focus each year, what people tend to forget though is that it's not the only cycle race each year, it is however the toughest.