My opinion: it depends on what you are trying to convey. If the original idea is to convey a sense of metaphysical existence of a personal god or gods, one should use いる. If you are trying to convey the sense of a historic or customary association of a god with a certain place or activity, you might use ある without any resistance from the listener.
Since Japan tends to be less dogmatic about religion, you will find a spectrum of opinions on this, and not much agreement on linguistic orthodoxy. In English, we get very squeamish about god vs. God, or him vs. Him, because a large and vocal segment of the population will get upset if the wrong spelling conventions are used. I have never heard of the Japanese expressing a similar sense of outrage at the use of ある vs. いる, although in some contexts I think it would be slightly weird to use ある instead of いる.
I've checked in a corpus. ある seems to be used often for the existence of the concept of god. Other than these differences, Majestic-san's and mine, in meaning, note that ある/あり (or なし for negative) used to be used in classical Japanese not only for god but even for people. So, it still remains, for instance in proverbs or set phrases.