Leca pebbles are really for use when growing orchids or in hydroponics, in other words, soilless growing, so they won't stop the fungus in your pot, it'll still be in the soil, you just won't be able to see it beneath the leca (the fungus won't grow on the leca).
Fungus grows in pots because, as you've said, there are moist conditions most of the time - usually its there because its decomposing material within the potting medium, particularly woody parts, no matter how small they are. You might also see fungus in the soil (if its damp all the time) which is actually associated with the roots of the plant, helping it to grow well in a symbiotic interaction - this is not usually visible on top.
I'm afraid, if you want to stop this, its out with the self watering pot, repotting into something with a drainage hole that you water yourself when necessary, rather than trying to kill any fungus present. This answer assumes the plant is perfectly healthy and growing well.