I think the best and easiest idea is to prevent people from carrying weapons on airplanes. Taking over an airplane with special underwear is not a realistic threat.

In contrast, trying to interview and run background checks on every person boarding a plane to figure out if they are an extremist on a mission or not is (a) much more invasive, and (b) much less likely to work out. Especially when you actually don't want to prevent fundamentalists from flying on planes (I don't think preventing some major evangelical church leader or some radical rabbi from flying would even be constitutional, and clearly not a popular move if attempted).

Note that I am not at all advocating for extra security targeting of Sikhs or any other such religious or ethnic targeting. I am just saying that no one should be allowed to carry a weapon on board a commercial airplane, for any reason.