The reason the eldereldar let humans become so powerful despite having farseers is that farseers have limited capacity to predict the future, and the eldar are, ironically, horrifically short sighted in their actions because of this. allAll their actions are taken based on farseeing, completely ignoring obvious extrapolation on what will happen afterwards.
Typically, after a number of years, Seers pass to some other life as part of their quest to explore the rich possibilities of the Eldar Path. However, some amongst their number can end this journey by adopting the mantle of the Farseer which leads them being trapped on the Witch Path and thus unable to change their future role. Thus, these individual Eldar focus their remaining years on learning and exploring their psychic powers. Much of their time is spent casting Seer Runes whilst making endless calculations and prognostications where they attempt to guide the fortunes of their Craftworld. This sees them attempting to discern and anticipate the future by watching out for difficulties that lie ahead in coming events. As their calculations are based on predicted events that can be hundreds of years into the future, their immediate effect can be hard to determine. Despite this being the case, Farseers are seen as a vital part of a Craftworld who base all their political decisions around their predictions.
-Warhammer 40,000: Compilation, pg. 53 – Warhammer 40,000: Compilation, pg. 53
As you can see from the above, farseers are limited to "hundreds of years". As others have already pointed out, the time scales involved were actually in thousands of years. byBy the time the eldar figured out humans are going to be a problem, there was nothing they could do.