You're totally right. Now that I think about it, zero-tolerance always equates to zero-thought, as the point of zero-tolerance to create a shortcut through judgment and rules.
Zero-tolerance, in schools anyway, is zero-thought for the administration and principles, having to deal with the grey cases, setting exceptions when they're education administrators not lawyers.
I doubt a student who did a similar action (stealing and returning a library book) would perceive themselves as morally wrong even with a zero-tolerance policy in place on 'stealing'.