The whole plot of EX4 is developer's informational and mentall acrobatics to justify the idea "Geno is bad, Mercy is good *insert chad vs soyjack meme*".
If you compare circumstances of SHRIFT with game like Undertale, you will see how "mercy" ideas are different.
In Undertale, it was like "Yes, maybe monsters a little bit rude. Yes, you have all rights on self defence. But dude, they are harsh because they literally HAVE to be harsh. And yet, the most of monsters don't want to fight at all and will stop attack you after a conversation or another interaction through the battle. Characters like Asgore are even near mentall breakdown because of the sin's burden. So, you have power. You have your determination-thing. Maybe you will use it to broke this circle of violence? Maybe you will supress your urges and show some MERCY?"
In SHRIFT it is like "YOOOOOOO, WE HAVE KILLING MACHINES HERE!!! They killed sooooo many people!!!!! Like Archne!! Do you like our favourite edgy wannabe-predator??? Yes, i am talking about the one w̨̫͎̪̣ͅh̨̖͓o̢̬̭̫̥͔ ş̫̮a̡̘̜͙ḑ͕̪ͅį͙̭͇ş̮̙̗t̲̩̱̘͢ͅi̜͉͢c̡̘̮͕a̢̩̖̣l̨̥̪͉͖l͚̞̳͚͜ỵ̡̮͈̫ k̢̬̫̬͖͍į̪͔͙l̗͈͢l͕̦̦͜s̨͇͖̫͔̭ p͚͓͔̜̜͜ę͚̦̲o͈͔͖̙͉͢p̧̟̞̗̟͚l̢̖̟̰͙ȩ̬̮ a̩̮͜n̨̫̟̰d̢͎̟ f̨̫̤i̡̞̬l̥͓͢l̢̝̣̯͍s͉̞̲̲͜ t͕̯͈͜h̤͙͓̳͜e̞͍͍̩̖͢m̙̗̘͎͢ͅ w̧̦̣i̧̩̣t̢͓͉͚ḫ̡̠ͅ f̨̩̩̬͍̠e̢̥̖͖̥ą̦̤͈͉͈r̢̮̦̲͉ t̢̪̞ǫ͙̥ m̨̖̖̪̣̪a̡̲͇̮͍̟k̘̟̮̣͜e̡̘̪͕͉̮ t̡̫͈̱h̡͈͇̥ȩ̰̟̯̪̫m̨̦̥͇̙̝ m̧̫̪̲o̡̬̥r͎̗͜e̠͈̪͜ ş̫̳̫a̢̞͇̳͙͙t̨̥̬i̧͍̟̬̣ş̙̟f̧̖̮y̧̰̝i̢͖͓͎n̖̝͢g̢͙͔͕̟̠ ţ̬͉̘̭o̢̝͚͉̘ e̢̲̭a̡̘̝͕t̢̮̖̤ a̢͇̟̣l͇̱͜ͅị̡̳͎͖̖v̡̲̦͔̮ȩ̩̖!̧͎͕̱!͍̮̝͢ Like predators do in nature!!! Don't they? Sooooo... You are a good guy, don't you? What about some MERCY?
Huh? Are they going to change and stop killing people — you ask? You silly!! It's their nature ^_^!!!! Some of them even won't stop to try kill YOU
What do you mean "My common sense tells me that not ALL OF THEM are worthy for MERCY and i have an urge to commit genocide"? Why are you so mean ;(? I have that deep idea of pacifism and you are going to throw it out because you can't understand it? You stupid puppet of the Old One!!"
Undertale is about Mercy, SHRIFT is about pure Masochism. If you ignore information about world destruction and poor crying Kazuya, Genocide — is the best route. The only ones who i felt sorry about in Geno run were Lamplas, Empuse, Mother Rabbit, Hayakki and Echo.
Friendship and hentai scenes are temporary
But the Genocide is
ETERNAL