As far as I can tell, they're not directly analogous. Many of the things that are "abominations" to Nuggan are explictly allowed under Scientology (see below).
If anything, Nugganism appears to be a reflection of the state of Turkmenistan, where their eccentric ruler; Saparmurat Niyazov banned beards, gold teeth, the keeping of dogs and cats, lip-syncing, opera, ballet, circuses, smoking and makeup. Much like Nugganism, these bizarre decrees were read out on State Radio on a daily basis and added to a list of forbidden activities.
Given that this was a major story in the UK during the time that Pratchett was writing The Last Hero and Monstrous Regiment, it's certain that he would have been aware of it.
...followers [of Nuggan] are forbidden to eat chocolate, ginger, mushrooms and
garlic. - The Last Hero
Q. ARE THERE ANY SPECIAL DIETARY LAWS OR RULES AGAINST SMOKING OR DRINKING IN SCIENTOLOGY?
A. No. There are no dietary laws whatsoever - Scientology FAQ
Her mother had taught her to read, which was acceptable to Nuggan, and
her father made sure that she learned how to write, which was not.
A woman who could write was an Abomination Unto Nuggan, according to Father Jupe; anything she wrote would by definition be a lie.Monstrous Regiment
Q. WHAT IS THE SCIENTOLOGY POSITION REGARDING WOMEN MINISTERS?
A. The Scientology ministry is open to men and women. Because people are
spiritual beings, gender of a minister is not an issue in Scientology. - Scientology FAQ
Pictures of living creatures were an Abomination in the eyes of
Nuggan. Monstrous Regiment
Watch videos of Scientologists like Fraser, an Art Gallery owner from London Scientology FAQ