Yes, it seems Kirk should know he is going to butt heads with this Flint character no matter what.
Trying to skulk around the obstacle is not a particularly good strategy here. Trying to win a pissing contest would
be a good strategy if Kirk from the start knew that the planet fell under his apparently very broad jurisdiction as a frontier lawman - as a Federation subject aware of the overall power of the Federation, Flint should consider long term consequences and yield to Kirk's authority, regardless of Flint's powers.
But does Kirk realize Flint is a Federation citizen on a Federation world? Kirk chooses the planet by taking some sensor readings, and indicates no familiarity with it whatsoever: it's just "a small planet in the Omega system" to him.
(Incidentally, would that be the same Omega system where Captain Tracey found a way to live long and prosper? These single-Greek-letter designations are no doubt abbreviations - but in theory, there's nothing to say that this couldn't be the same system as in "Omega Glory", an episode without a stardate. If the Exeter
incident has not yet taken place, Kirk could easily overlook the goings-on on planet IV, as he enters the system with rhyetalyn blindfolds on. If said incident is in the past, ditto - and during the incident, Kirk would have had no reason to pay attention to planet III and the one hermit living there, possibly shrouded from cursory sensor scans.