The plan of ending humanity was deduced by Mettaton and Undyne because of the Player's actions (as the player is the one using frisk to do the genocide route in the first place, and you are even allowed to stop it at any point until mettaton, there's nothing keeping you from ending it.), Chara is simply the one watching and using narration to go throughout the route. Chara does not have any control over frisk, and they are simply just there to watch and eventually overpower you in the end, destroying a world that was essentially already empty. Remember, Frisk, Chara, and the player are all separate, and the player is the only one who has control of Frisk until the end of the genocide run. Not only that, LV has the power to make anyone evil over a period of enough killing, so if Chara is evil, both frisk and the player are evil upon completing the Geno route, and that's the one people normally take Chara from, which is not right considering that there is a ton of other evidence of chara's morality in other routes.
Regarding the gender of Chara, just because you can choose the name does not change the fact that the canonical name is Chara, who is They/Them in the story, with no dialogue suggesting otherwise.