If Precogntion works in the 40K way, rather than the normal Exalted Way, then it should work just fine.
Active Essence use can mess with the Loom of Fates' simulation/plan for the future because its programming doesn't fully incorporate the variables involved. This is the normal way precog is done in Creation, and it alone has this specific limitation. This does not hold true for all kinds of Exalted Precognition. There are Samsara linked precog effects which are infallible, and there's, IIRC, precog based perfect defences and surprise negators that also always function without fail, whether the enemy uses essence or not.
Warhammer Precogntion is not based on simulating or anticipating the future in a way Essence can mess with. It involves time travel. You literally look forward in time to see what happens in future timelines, because the Warp is outside of time, so you can look in at one time and look out at another, just as starships can enter the Warp at one point in time and enter at a much later or earlier one. Essence use shouldn't have any effect on that, and more than by default essence use stops someone knowing what you previously did - as from the privileged perspective of the Precog, your future actions happened in the past in their personal timeline of perceptions.
Being outside of Fate just means you're not modelled in the Loom of Fate, not that precog generally doesn't work on you, as non-Loom based Exalted precog charms do work on such people.