The Twins did separate secular/religious rule, and I think that the current awe with which the Tarshites hold the Shaker Temple partially reflects that historical positions, but I think that the replacement of the Sorana Tor rites with the Feathered Horse Queen rites to become King of Dragon Pass weakened the power of the temple in recent generations.
Remember that during the first civil war the Shaker Temple put forward its own candidate for the crown of Tarsh: Erantha Gor (presumably confusion by the CHoDP writer with the war goddess she followed). So there seems to have been no rules against a queen. They changed tactics to incarnate Sorana Tor and thus become 'kingmakers' after military defeat by Blond Arim (who had Lunar magical support) and the sack of the Shaker Temple by Lunar sorcerers.
That defeat dissuaded them from further attempts to crown a queen - but IMO there is nothing to stop you writing a story about a new attempt to raise a queen, in your Glorantha (though there might be considerable difficulties that might have to be overcome by heroquesting).
"Give the kids tools, so they can go build their own houses; not the blueprint of what the houses should be." Tori Amos
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