"They should be given the win since their result is actually valid for qualifying purposes."
This statement is simply not true. The course would have disallowed their time. Further, take the results to get it verified for Trials consideration and explain to them that you only have a gun time and no chip time even though chips were used and see how far you get. The race directors may not have questioned whether the course was run completely, but an outsider might question it. Race directors really had no choice but to do what they did.