The probability of being Muslim is a lot higher (about 1000 times more?) than of being Scientologist, so I presume you're talking about how many incidents you'd expect to have heard about per capita.

That's one adjustment that needs to be made, though not the only one. The other major adjustment that needs to be made is for proximity. That goes in the opposite direction. But it's not worthwhile thinking about it with current data - the energy should be spent on getting better data. I just did that for Afghanistan. 38,000 is the most recent figure I found for dead Taliban, who I interpret as seeing themselves as fighting Islamic jihad, seeing as the Taliban is an Islamic theocracy. Divide that by 1000 and you have 38 Scientologists who, going by your figure, need to have died in armed struggle with - I don't know - the police, maybe, in order for Scientology to match the proportional death toll in religious violence. I'm pretty sure that if 38 Scientologists had died fighting the police, I would have heard about it, even though I didn't specifically research the question.

And the Taliban is I think just a small part of everyone who died in the last decade in what they considered to be Islamic jihad.

Update - the factor of 1000 is way off. It's 25,000 Scientologists versus about 1.5 billion Muslims. If, say, 150,000 Muslims have died in armed jihad in the past ten years, then that's one in 10,000, which comes to two Scientologists who need to die in armed struggle to match proportions. So being a Muslim is probably not significantly more dangerous than being a Scientologist. Further information could reveal that it is less dangerous.