Sin will prevent you from rejoining a previously abandoned creed, and their respective, default sanctuary NPCs will react to your denouncement, some of them refusing to offer their services. Desecrating a sanctuary is much more serious; you lose the abilities to teleport to, heal at, level up at, or take oaths to any sanctuary of a creed you have desecrated, and you will be attacked upon entering.
You can absolve your sins by seeing the Candlelit Lady at The Watching Woods who can forgive your sins for a price. It costs 1000 Salt for each time you change your Creed, and 10,000 Salt for each time you desecrate a sanctuary.
Take note that you need to desecrate only 1 sanctuary if you want to take multiple sanctuaries from the same faction. After the first desecration the faction will automatically aggro on you, which will allow you to defeat the sanctuary guards without using multiple Stained Pages or collecting tons of sin. Example (Tested): You start the game with The Iron Ones claim multiple sanctuaries and then switch to the Order of the Betrayer. Desecrating single sanctuary (and gaining single desecrating worth of sin) will make The Iron Ones hostile. Now go to all the Iron Ones sanctuaries fighting the guards and claiming them for the your new allies (while collecting Expunged Hearts). When you're satisfied you'll only need 10,000 Salt to undo the sin.