In modern Japanese, it's read ぐんしん most of the time.
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.
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.)
The 9 individuals mentioned were named 九軍神 and there might be a customary way to read it as a proper noun. I don't know if it's きゅうぐんしん or きゅうぐんじん, but I'm pretty sure it's not きゅういくさがみ.