Human history aside... (given everyone in this thread seems to generalize rather than give concrete evidence of how genocide affects diplomacy at different eras of civilization. Culture, time period, global circumstances/realpolitik -- there are simply too many factors at play for simple handwaving.)
From a game mechanic perspective, the penalties for purging SHOULD be severe. Ethic divergence is one of the key problems this game introduces, which creates long term unhappiness maluses that propagate (as there is a chance when a new POP is created, it uses the diverged POP's ethics, and unhappy POPs could migrate to another planet and spread their ethos). Even when running an planet with -60% ethic divergence in my games, it often takes 30-50 years to bring any significant number of diverged POPs back to the official ethics. That's decades of unhappiness malus (for your own people) or, in the case of conquered foes, decades of faction unrest and potential for rebellion. To make things worse, those unhappy, unproductive POPs gives you reduces resources for your troubles while also penalizing your tech.
Purging can solve this entire problem immediately, and is an extremely powerful 'shortcut' tool to deal with what is otherwise a long-term headache that forces empires to slow their expansion. It's why despite the hefty diplomatic penalty, many veteran players still find it effective to play fanatic purifiers via purge-assisted fast expansion.
Stellaris is a game where the devs spent a lot of time emulating the headaches of administrating a far-flung empire that inevitably (tries to) grow in diversity. If you're going to take the shortcut by hitting the PURGE button every time something unsavory pops up, then you should take the consequences for it.