In modern Japanese, it's read ぐんしん most of the time.
It looks like the term means "legendary war hero [who was human before dying]" and "deity of war [who is always immortal]". I feel like in the latter sense it's more likely to be いくさがみ.
http://doi.org/10.15024/00002106 gives a summary on the old usage of "ikusagami". (I don't know if the author intentionally avoided using "gunshin" and "gunjin", though.)
Between ぐんしん and ぐんじん, ぐんじん may be an old variation or even a more standard way to read it a while ago, but it's mostly replaced by ぐんしん now. It doesn't help that 軍人 is also read ぐんじん, and used in similar contexts.