The church is a public benevolent organization and thus needs to uphold its reputation. Tinies shrunken by Goddess Aila are far more durable than usual. They also shrink everyone in close contact with them for a month(though there are ways to avoid this) and everyone who leaves them with a fatal injury. It's also possible to revive them within a day after their death if they died on sacred grounds(which includes the whole church).

About mages: shrinking magic is pretty common and is used pretty often, although human shrinking magic is easy to resist, has an expiration date, and can be dispelled. Elven magic is a bit more remarkable, although it's just the same magic, they just use their larger amount of mana and its higher quality, thus making it slightly more reliable. Divine magic, however, has only the downside of needing a ritual. After being shrunk, other size magic will not affect you and it cannot be dispelled at all.

About different sizes: Half her foot is Goddess Aila's preferred size, so it's the default when shrinking using her rituals. She's very reluctant to grow people back, so if her nun shrinks, it will probably be something permanent, so no one tried exploiting her rituals that way yet. On another note, there's a secret prison room, with people who committed crimes against the church are shrunken to the size of the toes of the nun who apprehended them.