Both shrines and temples are made - consecrated - through the Consecrate spell. Note its description: 'The consecrated sphere is sacred to the spellcaster's god'.What this means is that a Rune Priest is giving up their power for other people. How different is that from real-world religions?! Real-world religion takes. It takes money, in the form of donations and inheritance from the deceased. It takes time, attendance at mass and prayers from the faithful. Of course, the cults in RuneQuest take time and money too, but you'd never see a bishop or metropolitan physically reduced by their devotion. Of course, one could reason that devotion to a delusional belief system is reduction enough, but the distinction is real. Importantly, an archbishop probably isn't aware that they're delusional.
A temple, then, is a site that is the subject of numerous and sustained Consecrate spells, kept in place by the presence of the permanent clergy.
Shrines are much smaller and local, their consecration kept in place by a sole Rune Priest responsible for that area. A shrine's consecration may lapse; it may not. It will depend on who looks after it and what else he or she has to do.
Creating a shrine or temple is thus a case of casting Consecrate on an appropriate area, object or building and then maintaining it. Once cast, its ties-up the dedicated POW used to cast it, putting it beyond other use (spells, usually) so a single person could maintain a shrine within a certain range if he has no other duties requiring dedicated POW or magic.
So the answer to your question: 'A character can scratch a holy symbol on a rock, or just wave his hands and say, "it's a shrine!", or what have you, and the location works as a shrine forever after' is Yes, sure he can. But he must cast and maintain Consecrate to keep it that way. If he doesn't, and the spell lapses, so does the ability to use the shrine to recover spells. Furthermore, a shrine must be recognisable to others of the same faith. Scratching a symbol on a rock might work in one culture but not another. Something recognisable and visible is going to a) declare that god's presence and b) help the divine follower find it and use it.
However, shrines, being local and personal often aren't enough. That's what temples are for, which typically contain numerous shrines to a pantheon's gods. Grouping them together under one roof makes consecration easier, attracts maximum attention, makes a political and religious statement, and so on. (Lawrence Whitaker)
A better analogue for real-world religions in RuneQuest is the Empire of Wyrms' Friends. Some of their cults literally suck the life-energy from its members to feed the Cosmic Dragon. This is much closer to Hillsong or the Church of Scientology that take money (i.e., power) and must obviously give something in return, though I'm not entirely sure what. The veneer of community, perhaps?