There is a marked difference between Basterd violence and Nazis violence, the most obvious is that Tarantino plays the Basterd violence for laughs. You are meant to enjoy it, enjoy the revenge but also it acknowledges the difference between the Basterds' motives the Nazis. We not only laugh when things are funny, we also laugh when we are uncomfortable - this cartoonish violence makes us uncomfortable because these acts are still being perpetrated on humans - villains or not.
There are only two actual acts of violence perpetrated by Landa on screen one is the massacre of the Dreyfus family which is cold and impersonal and played very straight. At no time does Landa even truly acknowledge their humanity with no reaction or display of emotion. He is cold and clinical in his questioning of La Pedit and can only compare the Jew to a the rat, dehumanizing an entire race. The other is when Landa strangles Hammersmark, this is Nazis on German violence and it is done in the most intimate way possible - by Landa himself and he is obviously affected/stimulated by it. He has killed a person, a traitor no doubt, but he even comments on her death to Raines and in the process humanizes her.
The entire reasoning behind Raines' campaign of terror on the Nazis is based in their inherent humanity - the are obviously meant to have feelings and he and the Basterds are, obviously, meant to affect them. The scalping and the brutality cannot deny or erase the fact that even the Nazis are people in fact it only heightens it. Even in revenge - Raines and the basterds are better people than the Nazis and their actions, however brutal, are more noble.