One idea they are suggesting is that the impact that created Charon and the other moons was much more recent than expected. If so - then perhaps the interiors would still retain heat as a result of that impact.
As for smaller impacts - yes they do deliver a lot of heat to a planet. In calculations for Mars they worked out that a large impact onto the polar regions could create a lake that remains liquid for a thousand years. I think that was an impactor of order 10 km or so not that huge. Quickly gets insulated by the ice that covers it, and the impact heats up the rock below the surface so creating a resevoir for heat and a hydrothermal system - that's for Mars would need to be adapted of course for Pluto.
I'm no expert here. Just to say your idea seems to have some merit to me :). The experts seem to be pleasantly surprised and puzzled, expect they will be looking into a wide range of theories to try to explain what they see.
You might also be interested in this interesting suggestion that perhaps Charon formed by fission of a rapidly spinning early liquid Pluto and convection of lighter fluids to the surface rather than through collision.