I like your approach Rurik and may well use it myself. I have been toying with a couple of ideas myself.
1) Minor Runes/Cult Runic associations - Upon being initiated into a Rune Cult, a worshipper is paritally attuned to his god's runes. This association allows them to build a Runecasting skill and learn Rune Magic associated with those runes. The character does not get the runic powers gained by attuning a proper rune. Nor does this runic association have a physical form that can be removed by some corpse-robbing "pelado" for his own use.
2) Runic Prohibition - this is a bit obvious but I've come across GMs who don't seem to use it. Most cults have, for want of a better term, Anathemetic Runes (i.e. Most Troll cults hate Fire/sky (except them Zorak Zoran weirdos) Yelm worshippers hate Darkness etc). Any attempt to attune such a Rune will excommunicate the worshipper and invoke a Spirit of Retribution. (Just say "No", Kids!) The exception is the insidious rune of Chaos, see below. Skybolt is now associated with Storm in my game so that loyal Orlanthi can still use it (as they should). If a candidate for initiation has already attuned a forbidden rune, he will be denied entry until he has undergone the Ritual of Severance for that Rune.
3) Chaos Rune - The importance of Chaos to Glorantha requires special consideration. Anyone can attempt to attune the Chaos rune regardless of cult prejudices. However doing so will cause the individual to register on Sense Chaos as the character in now tied to the Chaos Rune. Worse yet there is a POW x 1% chance that the hapless attuner will develop a Chaos Feature. As noted above Skybolt is now associated with the Storm Rune, but Chaotic's have access to the Spell Entropic Blast, which is Sky Bolt with the serial number filed off!
4) Ritual of Severance - This is a universal ritual known by almost all Cults and Orders. It involves a full day of fasting and meditation or chanting & trance-work (depending on the nature/preferences of the Cult) per Rune to be severed. At the end of the ritual the Runes focussed on are disassociated. The Player must also roll above the appropriate Runecasting skill to see if it survives in a useable state. The higher a players skill the more "tuned-in" he is to the rune and the more traumatic the process of severing it. He does not regain the POW spent to attune the Rune as it expended not just tied up as it would be for a Rune Spell. It is not a Ritual undertaken lightly and is usually done to get rid of inappropriate runes prior to advancing within a cult.
The Chaos rune may be severed, but the Cult will usually demand a quest to prove the recipient is suitably contrite. Of course certain cults such as Storm Bull or Zorak Zoran will only offer the simpler, more efficient solution of Decapitation or Dismemberment, but that's the kind of fluffy guys they are!
That's my two-penn'th anyway and apologies that it is longer than I expected!