I don't think that Muslim Terrorists will be showed up in the same way as the Nazis were in that episode. So far those terrorists have had a minor impact on the world history
Remember also that the Soviets killed 60 million people between 1920 and 1955 without resulting in any"space Stalin" or "space commies" showing up.
I think the reason that the Nazis show up the way they do in certain episodes are that they are so easy to set up as villains. The crimes they did, the uniforms, leader cult, racist policy and general behavior makes them somewhat believable as enemies. Not to mention that they were so totally defeated and their crimes so openly revealed as well.
And don't forget that the series was made in the 60:s wehn WWII wasn't so far away and at that point there were no Muslim Terrorists, the cold war between the US and the USSR was not as "cold" at that specific point and there were no other "evil power" visible which could be transformed into the Star Trek universe.
Still, I agree that the episode was over the top with those stereotype Nazis. With all respect to TOS which I actually like very much, it was simply a badly written episode.
When it comes to portraying people lead by evil ideologies, I'm more impressed when they take the ideas and actions of the Nazis (and maybe similar attributes from Soviets and terrorists too) and use them for some future hostile alien regime without putting on Nazi (or Soviet) uniforms or without using 20th century Earth symbols like the swastika or hammer and sickle for those aliens.
I did watch a Stargate SG1 episode some time ago when the team was sent to a planet where the people asked SG1 to help them fight some merciless enemy. At the end of the episode it was revealed that those who wanted the help from SG1 actually had the same values as the Nazis and had actually started the war which was going on. I did find the aliens in that episode more scary and repulsive than the rather comical Nazis in the TOS episode.
They were called Troglytes.