Er, you do realize that you've blown yet another hole in your notion that "intrinsically evil" (which you still have not defined in a manner more satisfactory than Borges' Chinese animal classification)?
How can you possibly justify empowering the state (I don't spell it with a capital letter, as I do not consider it to be a Deity) to punish someone for taking the "proper action", as that is clearly antithetical to the "common good"?
The State would not punish the liar in this case because the lie was committed under duress. (In your case, the person harboring the Jews had three options, not answering [which would result in arrest or execution for him], handing the Jews over for certain execution or lying [which would save the Jews' lives]. Choosing the final option would be the best option given to him under duress.) The courts commonly take duress this into account, as when someone is forced at gunpoint to take cash out of the till.
...as that is clearly antithetical to the "common good"?
Lying under duress in your example serves the common good because it saves the lives of the Jews, which is obviously preferable to lying to the Nazis.