I don't believe he was stationed in Jordan or the middle east. There was no mention of being a dual citizen in any news article I read. And although not a crime, how can it permissible to hold dual citizenship and have a TS or higher clearance. I don't dismiss your analysis. But where is the official investigation/dismissal of the appearance of malfeasance? After Ft Hood are they still gun shy about investigating Muslims? That is my point.
The article said he was stationed in the Middle East.
It isn't permissible to be a dual citizen/hold a foreign passport and have a TS clearance but believe it or not it can be hard for US investigators to check. Other countries are under no obligation to report that to US investigators and even if they did it may not be reliable due to their own government bureaucracy and/or privacy rules. Then there is the other nation's citizenship laws, some countries will not allow you to renounce your citizenship or recognize it if you do (so yes, in a technical sense someone can still be a dual-citizen and hold a clearance but you can't actively take or use any of the privileges of the other citizenship, that includes a passport, or otherwise show 'dual loyalties'). So while they probably went the extra mile to check this guy's background, or at least they should have, it is quite believable he was able to hide the fact he had a Jordanian passport.
I am not sure what you are referring to when it comes to 'investigating Muslims'? Are you referring to clearances or investigations in general? The guy you are referring to was investigated and is in jail, it doesn't look like being Muslim was an impediment to that. If you are referring to clearances I can assure you that the investigation is thorough no matter the background, if you have a background that calls for more thorough investigation it will happen and I have seen it first-hand repeatedly.
When it comes to clearances and counterintelligence threats there are a lot more realistic threats than religion, the biggest one being simple greed mixed with ego. If we were to take religion into account then maybe we should look at Russian Orthodox and Jews in addition to Muslims since both have been factors in more recent espionage cases that were very damaging to the US.