1) They are worried of bad PR from a headline being published that goes: "Apple encourages drug abuse with multiple apps such as Amphetamine".
2) They are worried of a lawsuit if it is found some app contributed to the sell of illegal drugs.
3) They are worried of parents complaints being concerned that they've found an app called Amphetamine on their kid's device.
And in some way, I can agree that as a Company, I'd rather not take my chances with any of them. Now, the policy being applied inconsistently is another issue. And ya, I wish the world wasn't so that a company needed to worry about these, but it isn't, so I'm not sure I can blame Apple that much for it. This also seems like a silly cause for them to champion.