The spots aren't actually fungus - they're the waste the fungus leaves behind. You can generally clean them perfectly with plain vinegar and a cotton bud, the tricky part is dismantling the lens without damaging anything and then getting it back together correctly, with no fingerprints and the minimum of dust.
I've cleaned a few Pentax 35mm lenses and had one professionally cleaned, the SMC coatings seem pretty good at resisting it. Get some quotes for having it professionally cleaned and add that to the cost of the lens, if the result is more than a mint example of the same lens then let it pass (unless it's incredibly rare).
The problem shouldn't reoccur providing that you store the lens in a breathable case, use silica gel bags, and make sure the air in the storage area isn't too damp. If you get condensation from sudden temperature changes or the lens gets wet then don't pack it away for a while - I tend to leave my camera on a tripod in the corner of the living room for a few hours where it'll be gently warmed and dried.