What were they supposed to do? Scramble jets and intercept/ force a landing?

YES!

Surely shooting them down if they haven’t faced a trial can’t be protocol, as a U.S. citizen that would be like blowing up boats and claiming they have drugs on them and not letting the people stand trial

Your comparison is bullshit and you should feel bad. The essential difference is that the US Navy isn’t even trying to give the falsely-accused fisherman a chance to surrender and stand trial.