I see what you're saying, but our thinking was that if you engage with these systems in different ways, you will get a different outcome. The core conflict is between the ship's AI and the entity and who "wins" that encounter is down to how the player engages in the dialogue system. The conflict isn't directly the threat of an enemy attacking you, but rather the question of who you side with in this cosmic horror situation. Which fate is least miserable? you resolve this with your actions and chosen paths.
It's a stretch I know but I'm glad we went with that route for the sake of atmosphere, adding a traditional combat system would be cool and we will consider it for future builds, but for this Jam requirement, we focused on narrative conflict. If that's too far of a reach for some people, so be it, had fun and learned a lot either way :)