I've only ever seen guides on this which involved exploits, but it is completely possible as a rogue to do this without using any.
Here are the rules:
1) NPCs spawn the elite guards, they don't just randomly spawn.
2) There are a couple of pats you have to watch out for (ie. Donnelly Firecask) who spawn guards if they see you.
3) The NPCs are tightly packed around the entrances, so you need a rogue (or maybe a feral) to get in. Hunter and moonkin stealth is not strong enough.
4) The ethereals in the transmog / reforge rooms and the bankers do not spawn guards.
Basically, this means entire areas in the shrines can be ganked in. In the Shrine of Two Moons the portal room, bank, transmog room and the inner walkways are kill zones. It is harder in Shrine of the Seven Stars as the pats have further routes and there are NPCs in the bank and portal room which you have to stay clear of, nevertheless still entirely possible.
5) The elite guards can be escaped from, use trinket or vanish on one of their nets, then use rocket boots, and sprint after that if necessary. Either head for the steps and goblin glider off, or run along the walkway to the other side of the shrine. Make sure you are vanished if you are going to run past other NPCs or every one that sees you will spawn another elite guard.
You can see this, done hardmode in the Shrine of Seven Stars, in action here:
Now go forth and make rogues feared in cities once again.