This is mostly speculation, based on how the Dark seems much more aware of latent others than the Light. The main character, Anton, is revealed to be set up in the climatic showdown (remember in the videogame how the badguy was initially killed by Anton, but he worked it through to discover a thread in which he won and then played that scenario out for the real thing) but I think even more so Anton was set up by a bargain between the badguy and the lead good guy who healed Anton. Anton would have probably declared for Dark, but he was specifically set up by a bargain between those guy as a form of live bait, the dark sacrificed a potential warrior for a particular deal we don't yet know of, but the dark also realized (probably through a more complete prophecy than we're given) that Anton was the father of the foretold 'great Other' The dark therefore connived a way to get Anton to estrange himself from his son but to keep the son alive (the bargain with the light to use Anton as bait to catch the witch breaking the truce, wwhile the ligh was unaware of Anton's Other-ness). Because Anton would be 'rescued' by the Light, it would also implant a dark-inclined warrior in the Night Watch, and would give the dark a trump card if Anton were ever likely to encounter his son before his son declared.

So I think the real conflict of the overarching series is not the light triumphing over the dark, but a revelation of a terrible power structure and exploitation of the Others by the 'truce' government they've been living under. Much of the movie hints at problems with 'crimes' of the soldiers and how this ruptures their relationships again and again as they enforce perhaps unjust laws and follow brutal orders. It's not apparent yet, but this could be the first flowering of the Russian equivalent to Godzilla--the cultural working out of fears, angers and guilts from a recently devasting past that has since gone through a paradigm shift.. So yes the balance will be upset, but it will be replaced by a completely new more transparent system that is neither light nor dark.

I expect the next film, DayWatch, will focus on the boy discovering exactly what his father discovered in Nightwatch. In fact I expect it to end on a similar betrayal revealing the corruption of the system.