I'll attempt to answer.
Initially I thought you were talking about his punishment for carving a swastika into Landa's forehead. The answer is in the movie. Raine says that he'll be "chewed out" for this final act of retribution, but that he's been chewed out before and isn't concerned at the prospect.
However, the actual question seems to be "Why wasn't Raine tried for war crimes?" This is a fair question b/c the Basterds are indeed a special squad, sent in to terrorize the Nazi soldiers, and in doing so, do commit what amount to atrocities.
There are probably many answers one could give, but this is outside the scope of the film. Tarantino has said that he was making a "Jewish WWII revenge fantasy" and that's basically what he delivers.
It may be instructive to compare Landa to the Basterds, as all are soldiers:
- Landa actively hunts and kills innocent civilians with aplomb, and takes great pleasure in the activity.
- The Inglorious Basterds may kill civilians, such as in the film's finale, but this is in the context of collateral damage, and the civilians in this case can be considered complicit per their association with the Nazi regime.
In the context of the film, the Basterd's mission is perhaps seen to be justified because of the industrial scale atrocities committed by the Nazi regime, and their having started a war that resulted in the deaths of untold millions on all sides of the conflict.
However, your point that "'All Nazis should be destroyed' is the same thing as stating that 'All Jews should be destroyed.'" is incorrect at a fundamental level:
The Nazis wanted to destroy all Jews, Gypsies, Slavs, etc. based on their "race" (i.e. the ethnicity they were born into.) Being part of one of these groups was not a choice, and it extended to women and children. In other words, genocide.
Affiliation with the Nazi party was a choice, and although I doubt that all German soldiers were enthusiastic supporters of the regime, it was their ill fortune to face conscription in service of the Nazi agenda. Nevertheless, we are talking about soldiers and politicians, not civilians and children.