Sounds to me like you have a problem with the over-zealous enforcement of the rule, rather than the rule itself.
While I agree the enforcement can be over-zealous (I've seen it first hand), I think if it wasn't produce it would just be something else they'd nitpick. It's the mentality of the guards that's the problem.
And what type of system would you propose as an alternative? A threshold based on actual risk? Well then every type of produce is going to have different limits. And what about different sub-species of the same fruit? If Macintosh apples are a bigger risk than Red Delicious, surely they should have different limits. It's only fair. Now you're counting on a traveller (and border guard) to be able to know the difference between a myriad list of produce types. Good luck with that.
I'd argue, that such a system would lead to slower crossings, higher costs, and less focus on more important matters like security threats. The rule itself may be extreme but makes a lot of sense in the context of processing millions of travellers efficiently.
Just as with software, simple, easy to understand paradigms are usually better.
>If you're going to forbid apples you might as well forbid those otherwise it is inconsistent.
The line has to be drawn somewhere. In the interest of balancing risk and expediency "no produce allowed" seems like a perfectly reasonable rule to me. Even children can understand it. Heck, even non-English speakers could be made to understand it with some well designed signage.
Anyways, there are way bigger issues with border crossing rules and procedures. It just seems like an odd issue to be so passionate about in this day and age.