While I suspect a flood of Light could happen, and as pointed out the way the Allag empire stagnated seem to fit a something like overly dominant Light. I don't think there is a very high risk of that happening anytime soon though. Hydaelyn has been growing progressively weakened for thousands of years. Even with the changes we have made recently I think its a long way from totally turning everything around.
I think the Ascians calling on the Warriors of Darkness is more in response of losing their sense of control over us. I suspect that prior to this the Ascians have rather underestimated the WoL and seen them more as just another pawn. We would be far from the first WoL they would have dealt with. I think they are more actively trying to mitigate the fact their control over what's is going on is slipping as we get too powerful to handle.
I do think that balance is an aspect of FF14's story but I don't think the WoL is necessarily opposed to balance or darkness conceptually. Though it hasn't been dealt with in the MSQ, the concept of finding balance with darkness does pop up in job quests, the DRK obviously but also MNK touches on it with its sects of Light and Shadow. I suspect balance will be something that will become an important factor in the story eventually.