But if a US citizen in 1942 were to go and fight for the Nazi's, and lets say he became a high-up officer-- would we not be justified in going after his life "extrajudicially"?
No, we would not. We were already at war with Germany, so the solution would be to simply (and legally) kill him in combat.
What if a US citizen went to Mexico and became a higher up in the militarized drug cartels (lets not turn this into a discussion on drug politics)-- would we be justified in assisting in his death if capture were not an easy option?
No, we would not. That's a job for Mexico. As a sovereign nation, we have the right to defend our territory. If a violent invader crosses our borders illegally, we are perfectly within our rights to shoot them dead on sight. If they don't cross our borders, it's not our problem.
You seem to be confusing our recently ineffective justice system for a lack of justice.