How to you create a hive mind race

Stone Age primitives are actually a third state in-between the pre-sentient races that you can uplift and the fully sentient primitive civilizations that you can observe.

This is explained on the Stellaris Wiki's Pre-FTL Species Page:

There is a third possibility of non-FTL races, which are the stone age primitives. They appear as modifier on planets. If the policy for native interference is not Unrestricted, then the empire will be unable to colonise the planets. Therefore a pacifist or xenophile empire (or the fanatic versions) can't chose "unrestricted", and will be unable to colonise these planets.

So you might not be able to interact at all. Perhaps they will advance to the Bronze Age at some point and you can observe them. It's not clear if that's a possibility.

If you can colonize, though, here's what you can do once you get there:

Known Variations:

• Voluntarily retreat to Enclaves rather than contest the primitives for the land: Places a number of primitives on the surface map as tile blockers. Apparently these blockers cannot be removed, though they provide Social Science adjacency bonuses.
• Antagonize the aliens: fewer tile blockers
• Enslavement: No tile blockers. The new species appears as enslaved pops on the planet. The slaves can be emancipated, and integrated into the empire. Useful if a pop is neeeded to colonize worlds of the same type as their homeworld. Option is only available if slavery is enabled as a policy.

I think I actually had this happen on a planet in my current game, but I was confused because there was also a Pre-Sentient race on the planet. I uplifted that race, and was surprised to find that the Stone Age primitives continued to live in the reservations.

You can't get rid of the differing war philosophy penalty, because that is based on your empire ethics. Instead, you need to get enough bonuses to offset the penalty.

I'd have to do some testing to ensure that this is the case, but here are some things that I believe would help:

• Increase their opinion of you. You're already getting a +21 bonus. There should still be some levels higher than that, though.

• Some things, like a Non-Aggression Pact, will help not only your opinion, but give a direct buff to the Alliance negotiations. I think Migration Access may help in this way as well. You may not be able to get migration access, depending on your mutual ethics, but one-way is probably better than neither.

• You don't appear to be trading with the empire. Trading improves their opinion of you by +5, and may directly impact the alliance negotiations. I often just trade a few minerals a month for a few energy a month.

• Common rivals improve relations. Determine who their rival is from the Empire Contacts screen, and declare the same rival.

• Common threats improve relations. If they're at war with somebody, go to war with them as well.

• If you become significantly more powerful, you can increase the "relative power of empires" modifier.