If either side would win, humanity would lose.
Please notice, that this is not a "good vs evil" fight - the Night Watch was taking part in the Cheka repressions that tortured and killed thousands of innocent people (for "the Common Good" of course), while the Day Watch was responsible for the Renaissance which managed to pull Europe from the Dark Ages. If they wouldn't fight (with "blunted dueling rapiers" - as called by Anton), the world would fall to one or the other side destroying itself, creating either brutal anarchy with "everyone for himself" or the tyranny of Greater Good, where even selfish thoughts would be banned.
Nadia is a good example here - she is a powerful Light magician, but it is not guaranteed that she will remain as such: powerful Greater Ones changed sides (Merlin switched sides to the Darkness while Arina became a Greater Light One). In the end, both sides try to balance so that they (and by extension, humanity) can survive.
There is a lengthy discussion on this topic in Twilight Watch which confirms that they are trying to preserve the status quo:
'What are you doing in the Night Watch, boss?' I asked. 'Aren't you sick of it yet . . . after thousands of years?' [...]
'Then let's assume that I'd really like to finish off Zabulon,' Gesar said calmly. I thought for a second. 'That's not it either. In hundreds of years one of you would have finished off the other already. Zabulon said that fighting with magic is like swordplay. Well, you're not fighting with swords, you're fencing with blunt rapiers. You claim a hit, but you don't really wound your opponent.' [...]
'I'm waiting for a miracle, Anton.' I looked at Gesar quizzically. 'I don't know exactly what kind of miracle. For all people to acquire the abilities of Others. For all Others to become human again. For a day when the dividing line won't run between Other and human being, but between good and evil.' Gesar smiled gently. 'I have absolutely no idea how anything of the sort could ever happen, or if it ever will. But if it ever does . . . I prefer to be on the side of the Night Watch. And not the Inquisition – the mighty, ingenious, righteous, all-powerful Inquisition.'
'Maybe Zabulon's waiting for the same thing?'
'Perhaps. I don't know. But better an old enemy you know than a young, unpredictable freak. You can call me a conservative, but I prefer rapiers with Zabulon to baseball bats with a progressive Dark Magician.'