The use of a "show of force" by supersonic aircraft has variable influence on the ground
Could you, in theory, protect the border of a country from intruding
crowds by simply flying over them (provided the crowds can't down the
plane)?
To answer your question, no you can't protect the border by doing that -- by itself. Sonic booms are loud and cause discomfort/annoyance. If you flew very, very low, (50 feet or so) you might cause physical damage to people from the combination of sonic energy and wingtip vortices and jet exhaust.
If what you are protecting the border from is crossing, all the people have to do is fall flat, experience the discomfort, and then keep on doing what they are doing. It takes more than a transient discomfort to protect a border.
If, on the other hand, this show of force is a part of a larger effort that includes ground and air based people doing things to protect the border, it may act as a deterrent because it signals to the people that whomever is guarding the border will act.
Experience base for this answer
Military Operations, Afghanistan and Iraq. The show of force using jet aircraft to influence a variety of situations on the ground via non-lethal means was common once major fighting had stopped and the "restore some semblance of order" operations had begun with their ensuing civil wars / inter-factional fighting.
Sometimes a show of force was more effective than others, in that:
- sometimes it induced even armed people to back off,
- other times it was just more noise during a fight.
- While most were sub sonic (for political reasons) passes, I recall very
clearly one case where a supersonic pass influenced the
ground action very favorably. (By that I mean that the unit who requested the air support achieved their objective, the people they were fighting did not).