Agree - legally it's a minefield and not one you are on the right side of I think...had the search/delay be carried out by security screening staff on behalf of the airport/operator then there would be a good case that the delay was the fault of the airport/operator and therefore regardless of fare tariff a fact that 'they' delayed the passenger and caused him to miss the flight...
FBI? well one assumes that legally they were acting 'independantly' of the operator and therefore any delay caused is down to them not the operator.
Do feel the operator has behaved very badly...'shaming' is the only way, kick up a real stink up to the level of the national press etc.
Interestingly as it has been explained to me by IATA the 2 and 3 hour check in times are purely a 'guide' and not contractual however airlines seem to use them as the latter when it suits them!