Being rational does not presuppose you rationally analyzing your feelings. IMHO, you are irrational if you disregard your feelings in this day and age (when we know how hormones affect us).

Even in the example from the post, there are good reasons to hit back. For once, a person who goes around and hits people unprovoked will next go and hit someone else, potentially injuring someone. Such a person is an obvious risk to society, and while we have rationally set up mechanisms to deal with that (police, court systems), they are obviously non-applicable (no witnesses): rationally, you are the only one who can "fix" this. By our hormones driving the desire to hit back, we are going to teach that person that there is pain in this for them too, hopefully stopping them from doing this in the future (and incidentally, that's exactly the suggestion that works best with bullies).

It's no accident they put similarly physical male as the attacker: our natural reaction to a huge chunk of muscle attacking us instead would probably have our fear stop us from fighting back, and with someone much smaller, we'd probably feel safe to assert our dominance with a threat of violence instead of really hitting back (imagine a girl or a small kid doing the same thing from the article).

Basically, being rational means understanding that our instinctive reactions have their reasons, and that we should sometimes let them play out.

It's also worth noting that what we feel ashame of is completely environmental: as a trivial example, a cop having their wallet taken away by a criminal would likely feel more shame than a civilian would (and similarly for men vs women).