The only way to over water with a waterfarm is fill the resevior up past the hydroton (and that's just a guess as I've never tried it), you only add water to the white water line on the blue drain tube.
If you don't run the pumps 24/7 then that's your problem. You seem dead set on using the waterfarm incorrectly, and if so it probably won't work properly.
I've had 3 grows (with a wf), and I'm on my 4th now and have never had the air pumps off, and the only problems i've ever had were created by me (nute burn, deficencies, pH etc.).
This isnt even remotely like growing in soil, you cannot over water if you use the wf properly. Besides the fact that once your roots hit the water in the resevior, those roots are now in DWC (Deep Water Culture) and if you don't aerate that water, by running the air pumps, you may be drowning them, I don't know the answer to that. Before the roots hit the resevior its an aerated drip, so some of your roots will always get aerated drip, while others get dwc.
So if there is a problem, then it's with you and how your running your set up, nutes, turning off the pumps or whatever your doing diffently.
I've never had dark spots at the leaf tips, nute burn at tips but that is lighter (a pic would help diagnose your issue) but depending on which way the leaves are curling it could be heat stress, nute deficiency or something else.
I would suggest you use the wf as it's intended.
GoLdD
P.S edited to add, I hope you bought a better air pump because the one that comes with the waterfarm is a POS, as well as drilling dozens more holes in the pot portion of the wf.