Isn't se usually supposed to refer to the subject of the sentence, where is God here? Why not pro ea?
Yes, reflexive pronouns usually refer to the subject of the sentence or of a superordinate clause (if the subordinate clause is dependent), but there are exceptions ... for example, when it is logically clear that the reflexive pronoun does not refer to the subject ... or when it technically can't refer to the subject, like in this sentence: The verb is in second person singular, so a reference to the subject would have to be
pro te.
Pacifica wrote about that to some extent in one of her excellent articles:
THREAD: se-vs-eum-etc-and-suus-vs-eius-etc
Reflexives are also used when the person to whom an utterance/thought/intention, etc. is ascribed isn't the grammatical subject of the introducing verb, but it is logical that the reflexive be used because it refers to the one speaking/thinking/intending, etc. E.g. A Lucio accepi litteras, adventare suum fratrem = "I received a letter from Lucius, (saying) that his (Lucius's) brother was arriving". Even if it isn't said literally, it is Lucius who says that his brother is arriving.
Now, granted, this happens a lot more often with possessive reflexive pronouns, but you also find such examples. I would say you could get away with it in that sentence ...
pro se would be more misleading if the sentence started with
Deus concedat, in which case I would probably also prefer
pro ea (ipsa) there.