How do I deal with a candidate mentioning God twelve times in their application?

Regardless of my own faith, referring to god a dozen times in an application is highly unusual and rather unprofessional. Prospective PhD students, however, should have some understanding of the professional customs of the field. (After all, you don't go on at length about any other personal and non-work-related beliefs and preferences in applications, proposals, presentations etc..) If the rest of the application is very good, I might look past this. But it is certainly a glaring minus.

People in some Middle Eastern countries use the name of god so frequently that these words are becoming familiar even in the west:. Inshallah, wallah, ilhamdulillah, mashallah, yallah (i think) and probably a few more. For less religious people these are just phrases they use without thinking twice, but the more religious are quite conscious of their literal meaning when they say them.

So if the candidate is from the Middle East, it may just be a bad translation, or it means that the candidate is quite religious.

This is just anecdotical, but I personally have told several quite religious people from the Middle East that I have no religion and I have not gotten any (visibly) negative reaction yet. So I would not automatically assume that a religious candidate from these countries will have problems tolerating other views. These countries have different degrees of piousness too, and anyway if he/she moves abroad, they are probably aware that they have to adapt to their new environment.

Obviously the letter you received (if it was indeed from the middle east) was not particularly well-adapted to western culture, but then one might first need to become familiar with western culture before one can adapt to it.

P.S. as a native speaker of German, I quite often use Gott sei Dank (thank god) in everyday life. I would not use it in any formal letter because it is a somewhat informal expression. But it probably would not occur to me that using such a phrase might be culturally inappropriate.

There are several questions here.

First, most people consider their religious beliefs to be a private matter, though that is not true for all cultures. If someone is applying to a school that shares a culture in which god is "worn on the sleeve" then it would be fine, I guess, but in a cross-cultural application it might be unwise for the applicant. Not every place has policies such as yours.

Whether the person will be disruptive or not is unknown and you won't really know unless you have a conversation with them, provided that they are ranked highly enough on proper criteria to merit a close look.

In general, I would consider "disclosing" their religion to be benign and I would even expect to have to make some allowances for some folks so that they can carry out their religious practices. But proselytizing for a particular religion, whatever it is, would likely be disruptive. You might need to have some rules around that, so that people know that they have to keep to the job at hand when working.

As to the question of letting religion declarations influence your hiring decisions, I would adopt practices such as yours. Your religion is your business, not mine. Other, more relevant, things will influence the hiring decision.