If she actually did that, by all accounts she is his enemy. If the attack on the warship was a case of mistaken identity and the trap intended for someone else, she wouldn't be all mysterious and shit about what she had done and why it was done.
I doubt she is an AI, because no other signals were picked up by the warship's AI. I can believe divine powers can't be picked up via regular scans, but not when another machine tries to contact him.
If - and I say
IF - this was a David Weber novel, the "goddess" would actual be an AI tasked with protecting this star system and the descendants of human colonists that are purposely kept ignorant so they don't develop and start emitting various radio waves, which would then be picked up by hostile aliens. It would basically be the origin story (Dahak series, book 3) of the 'Safehold' series. In which case what actually happened was that the warship stumbled into the defenses of the star system, where it was assumed hostile and attacked. Still, the pieces don't exactly fit together for this type of a plot.