The article points out that the 2004 earthquake slowed down Earth's rotation by 2.68 microseconds, vs 0.06 that may slow down when the reservoir is filled at capacity, 50 times less. And the 2004 quake wasn't the only one in this century doing so (i.e. the one in Japan in 2011), and other events can have that effect too (extreme weather, glacier melting, changes in atmospheric circulation).

Overall it may be better to have a cleaner energy generation than a small change in the day duration. Because what we are doing with global climate is already changing that duration, and more things, and that will hit us before the effect of the Dam have a chance to be visible.