I have no problem with the prevalence of Mythos monsters in the Golarion setting. They simply represent another interesting foe to be overcome. Granted, the fact that they can be faced down with blade and spell may seem at odds with the nihilistic certainty of their victory that's found in Lovecraft's writings. But consider: in much horror fiction a similar amount of danger and menace are assigned to vampires, werewolves and demons. Yet these are things that Pathfinder heroes regularly confront and overcome.
Perhaps in Lovecraft's Earth there are no forces powerful enough to give the Elder God's pause. In that world, the humans are truly insignificant and when the Stars Are Right they will be blotted out without notice.
On Golarion, things are different. On Golarion, mortals go up to 11!
And if that's not to your liking, if you feel that the Mythos monsters have absolutely no place in an epic fantasy setting...don't use 'em.