That's one of the problems, although by no means the only one, of rigidly conforming to the runes/spells model of RQM.
For example, Extinguish is an Air spell, but I can't see any reason why it couldn't be also a Water, Earth, Darkness or Fire spell. Water can put fires out, earth can smother them, darkness can choke them and fire can conquer them.
The only common Water spell is Water Breath, so I can't see a problem with that being denied to Fire cultists.
But, for example, the Befuddle spell is tied to the Disorder Rune and in Glorantha, Chalana Arroy has the Befuddle spell and the Harmony Rune, so a cult spell is tied to an opposed cult rune.
To be fair, there are not many such spells and most of the problems are with existing runic connections in Glorantha, so the issue probably won't arise in other settings.
However, I would just scrap the runic association completely or widen it to allow multiple rune-cources for spells.