Ny downside/difference to Pkunk being absorbed by Yehat

SPOILER WARNING IN EFFECT FOR ENTIRE ANSWER

Given the nature of the question, it really can't be any other way.

First,

You actually can only convince them to turn back twice. Each time you use an argument they find persuasive that answer won't be available the next time they decide it's time to reunite. The third time, you're out of arguments that they'll accept and cheerfully fly off toward their destiny.

This is important, because

If the Pkunk attempt to reunite with the Yehat before you start a civil war by showing them the Shofixti are still around, the Yehat will absorb the Pkunk and you'll never hear of them again.

However,

if you start the revolution first, and then let the Pkunk reunite with their Yehat brethren, the revolution will end victoriously -- and when you're about to depart on your final assault against the Ur-Quan dreadnought, you'll be approached by a party of combined Pkunk and Yehat ships; the Yehat are now ruled by a Pkunk queen, and they'll be assisting their cousins in reaching enlightenment and happiness and transcendence. Oh, and they think you're about to get yourself into no ends of trouble so here's a dozen ships to help you out...

The Pkunk-Yehat conflict can end in two ways. If the Captain presents the Yehat a living Shofixti, the Yehat Rebellion will break out and the Pkunk will be absorbed, seemingly vanishing, only to return in the last moment as an integral part of their combined civilizations.

If the Captain fails to do so, the Pkunk are eradicated by the Yehat.

Sources: 1, 2