Most contaminants taken out by skimmers are bad indeed, no doubt about that.
I have run a 125 gal skimmerless acropora system for more than two years with no issues at all, every coral was thriving despite I held three big angelfish (annularis, imperator and xanthometopon), a big japonicus, one flavescens and many small fishes. The only drawback was very unstable and every change should be done very slowly, specially changes in their diet.
The point here is not what the skimmer is taking out, but the microorganisms that compete and grow in the skimmate. Do you know what happens if you let the skimmate sit in the skimmer cup warm in a humid environment that prevent rapid evaporation? I'll tell you: the skimmate turns turbid clear, just like the water you could find in a pond.
The skimmate holds the most efficient bacteria and microorganisms you could imagine: nematodes, rotifers, cocos, spiros...and ciliates, many ciliates (with use to be omnivore creatures). This is what we just want: efficient selected microorganisms able to prey on dinoflagellates which are on the first trophic step.
Just place some GAC on your filter/mesh to remove the bad stuff and release the stinky waters back to the tank, I'm sure you will be surprised.