If it's taking that long to settle, it will likely get cloudy any time it's stirred up in the future.
If you have some sort of prefilter, maybe put that on and run the filter, and put a bunch of floss or something in the media chamber. If it's so small it's still suspended, it probably won't do much harm to your filter/impeller.
you could also do a couple partial water changes, but that's basically just a more difficult version of rinsing/washing send after it's already in the tank.
I may have read it in Walstad's book (not certain), but as the tank gets established, biofilm will form on much of the substrate particles, and this will keep the smaller pieces clumped together, and reduce the likelihood of stuff getting stirred up later on. may be a while yet, though.