There are different levels of conflict in this story and they need to be addressed as interelated, then separately (or, if you like, the other way around).
On the man versus man level, Kino does confront people corrupted by the temptation of profit. But as a rule they are already that way; the pearl serves only as a catalyst to bring out the worst in them (but greed is already entrenched in their basic nature). In this category is the doctor, most evidently (and the thief he sends in the night), but even the priest, although his thoughts could be seen as just a fleeting temptation. Then there is the group of pearl buyers orchestrated by one leader, who then send trackers to hunt down Kino and Juana like prey. These people are corrupt, dangerous and indeed enemies on a Darwinist level. There are also unknown assailants, such as those who burn Kino's home and destroy his boat.
On a man versus himself level, Kino is also in conflict with himself. He wants to protect his family and keep it safe, but if he relinquishes ownership of the pearl before he finds an adequate offer, he knows he will be giving up his hopes for a better future for Coyotito, including his education. Should he take the chance to go against the system and 'win' or not? How can he know until his full hand is played? Kino's conflict is not really one of a conflict of loyalties but of weighing immediate risk against long-term benefit. He opts to take his chance at selling the pearl in the city, and then loses his son in consequence.
It is a bit late when Kino finally throws the pearl back into the sea, but it is his way of "making a statement." It is his last chance by a dramatic act to show the community where his true values are and where theirs ought to be. Note that as soon as the pearl falls to the ocean floor, it doesn't lose its lustre but the lust it provoked when in the hands of men. It is one with nature again, in its natural element, and harmony is restored.