@Remlpsum I think there's a fundamental difference between "Poaching" a Dragon and a Deer- One poses some serious threat to the population directly. I also think it's less that they'd rather someone not kill the Dragon, but more likely it's also so nobles and the Guild itself can get its fingers into the pockets of adventurers. If they hear they've been hunting absurd amounts of creatures or high level creatures, they may want the materials. Something similar happens in a LN I've been reading where the Protagonist would rather not turn in their materials since they're underage to be hunting, despite her 'familiar' hunting them all of its own volition.
Though, the Guild Leader is far nicer about it. "We'll buy it from you regardless, you know? It'd be a shame to let all those supplies not go to use since your familiar gets so many for you." or something along those lines. If they were in a more major town or in a much higher reputation/fame as Shirley, I'm sure they'd be trying to pressure the Novel protagonist all the same since Dragon materials are probably really sought after.
Of course, this is all assuming Malice where we've seen none. The Guild Master of Shirley is probably being pressured by higher ups, etc. Still doesn't excuse him being a douche to the Receptionist.