The hints were coming quick and furious, but the major points that were more than just points, but actual proof are as follows:
1. The Jedi temple on Coruscant was breached in Rebel Stand, and a Dark Jedi and several light-side Jedi were all on the spot when a wellspring of the Force burst out-- and both of them were able to tap into it equally.
2. Zonoma Sekot (from Rogue Planet) subscribes to a whole different theory of the Force that does not distinguish between light and dark.
3. Throughout the series, various Jedi, including Anakin Skywalker, ponder upon the fact that when a predator kills to eat, that is not of the Dark Side.
4. The final conclusion drawn in the closing the of the NJO is as follows:
The above is what the books say; what follows is my own speculation.
By deliberately splitting things into light and dark, the Jedi (and Sith) give polestars-- guides-- to follow. As long as you behave _exactly_ according to these rules, then you are following the Light side or Dark side-- ie. a completely unnuanced view of good and evil. That explains why so many Jedi are pompously moralistic, and why so many Sith are cartoonishly evil.
What if Luke Skywalker had struck the Emperor down? Not in a fit of rage the way Anakin killed Dooku, but solely to save everyone? Would he then have fallen to the Dark Side?
Anakin's fall was not because he wanted to save the one he loved; he fell because he allowed saving the one I love to be a rationale to commit atrocities as he desired.