Sacred Flesh doctrine applies to the upper levels of Amarr society, because, as Chosen and Righteous and all that, they're held to a Higher Standard than lower persons.
There are also very good reasons to frown at and prohibit cloning amongst persons of power.
The Mad Emperor for example. One of my/Kat's thoughts about that was that he may have had clones or was preparing some, such that he would be an immortal emperor, which would be greatly inconvenient.
So when he's disposed of, the Church interpret scripture and set things in motion such that that sort of thing cannot happen again. Saint Articus for example:
http://www.eveonline.com/news.asp?a=single&nid=2491&tid=2prohibiting cloning prevents malcontent/undesirable persons in power from coming back again and again.
Cloning for lesser persons is allowed, because they do not have as great a Duty and all that.
There's a few examples about it in the PF, people up to minor Holders have some form of clone. There's a chronicle, and also there's a thing ingame in the lvl1 epic arc.