I can understand those guy's frustrations, and if I were in a similar position I would ask to be transferred somewhere else as well. It is rediculous.
If the FBI wants to investigate those guys, they should have done so when they first applied for their J-1 visas when they were still in Pakistan, where the US embassy could have requested criminal records etc.
To stop them and detain them for questioning like that is total shite. Yes, the US has to be cautious, very much so, but if they are going to prove that they are not in a battle against Islam, they need to be a little more considerate and not treat every single Muslim as a terrorist. Be thorough in your checks, but do not create PR nightmares like this.
In the FBI's defence however, I must say that it is possible that they had gotten their visas well ahead of the 9/11 attacks and that realistically they would not have been able to perform as thorough a background check as in hindsight they should have