The question is whether we can avoid giving the punishment, and still credibly hold the threat of punishment against rational defectors.

I know this reaction is not rational, but still, my first reaction was: In such environment (where it is possible to tell the difference between irrational and rational crime, and punish accordingly), becoming rational means losing your "get of out the jail once" card, and that's not fair! The more rational you are, the wider range of your possible crimes becomes punishable. You are being punished for being rational.

Technically, a good person should not care about limiting their own crime range, and (if the good for everyone is their goal) they should be actually happy they have less chance to harm anyone. But still it somehow sucks to know that while I would be punished for doing X (because I am rational and see the consequences), other person would not be punished for doing a similar thing.

I guess this intuition is based on the real-world situations, where the psychologists are not perfect, the justice is not perfect, and therefore any rule like this has big chance to be heavily abused. (As in: If you have a good lawyer, your crimes will be declared irrational, and you will be sentenced to two weeks of group therapy. Meanwhile the average Joe does the same thing and gets hanged.)