Most of the current words seem to be derived from Sanskrit.
For example, ദൈവം, ഈശ്വരന് , ഭഗവാന് etc. comes from the Sankrit roots.
There is an "older" word for God - ആണ്ടവന് This word does not appear in Gundert's, but a related word does. അണ്ടര് - meaning god. Gundert gives two origins:
- അണ്ഡം (universe) -> അണ്ടം -> അണ്ടര്
- അണ്ണ (above) -> അണ്ട -> അണ്ടര്
I also noticed an interesting connection with another word അണ്ട (young bamboo shoot). Gundert says it comes from ആണ് + തൈ = അണ്ടൈ -> അണ്ട by means of some neat ആദേശസന്ധി. I think this will be a deep, male-centric, etymology for the god-word as well: God is the "Male Shoot" or the male form - the പുരുഷന് - of the godhead.
But somehow this interpretation seems very forced. If there is a word for the the male form, there should be a word for the female form as well - and I don't know of any. Also, the etymology given by Gundert indicates a non-sexist God - especially with the -അര് suffix, as opposed to the -അന് suffix.
Interestingly, one of the tamil words for God is ഇറൈ which also means "above".