Darker side of Portal? Wouldn't that be the fact that Chell pretty much has a few years to live (at best) before the assorted cancers, radiation poisonings and other sideffects of the various hazardous substances she was exposed to come to bite her in the arse.
Think about it - Assuming that the portal gun/portals themselves have no harmful effects (which is also possible), she did spend a good amount of time in rooms filled with toxic waste. She was in close proximity to a huge selection of various advance technology, all designed by a company that regards "safety regulations" as a mildly amusing joke.
And THAT'S before we consider that she was liberally drenched in various gels in the second game. You know, the gels whose sideffects you were being warned about throughout the game. You know, the white gel that's made with ground up moon rocks that happened to kill Cave Johnson.
So yeah, Chell is dead very soon...
EDIT: Well, yeah, the film was pretty great too. Good production values, though I'm not quite sure how she figured out where the Portal Gun was...