In this article they suggest the surface of Pluto may be geologically active, which would erase craters.

 

No mention it could be because of its' location in a very rarified region of the Kuiper Belt. It seems reasonable to me that the inner solar system would be much more battered by meteors, but the outer solar system objects are so far apart that Kuiper Belt dwarf planets would be very small targets and not have the cratering as the inner solar system.

 

Pluto's orbit is eccentric and orbits out of the plane of the solar sytem. Does the entire Kuiper Belt also have this inclination?

 

http://www.businessinsider.com/pluto-surface-photos-no-craters-geologically-active-2015-7

The Kuiper "belt" is more of a torus. The main population varies ~10 degrees from the ecliptic and the secondary population has inclinations out to 30 degree. So Pluto, at 17 degrees inclination, is well within the secondary population and passes through the main population quite a bit. The point is that over its long lifetime, it should have been impacted quite a few times. The fact that there is no evidence of this leads to the conclusion that something has erased the impact craters. This is augmented by the fact that they have found impact craters on Charon, Pluto's largest Moon.

Alternative explanations would have existed, for instance if small objects that create most craters concentrate more in the ecliptic plane than bigger, observed ones, do.

 

Though, such questions have been made obsolete by images of Pluto that show smooth glaciers covering partly craterized terrains.