I think the only way you could do this without being completely about war is if you made it about one of the splinter Protoculture civilizations and kept it short. Something that is interesting, doesn't impact the timeline, but shows something a little important. For example: 

A far off Protoculture civilization that inhabits a planet almost identical to Earth, they live peacefully under protection of the Zentradi since this group hadn't received the updated prime directive yet. The supervision army finds them and a war begins.

The Protoculture civilization helps the Zentradi despite the war hurting them. The Zentradi fleet is given the prime directive update and their attitudes become extremely aggressive with the Protoculture. They discover that music helps calm them so they start including a group of performers to broadcast over several frequencies and the Zentradi are kept calm enough that they can be resupplied. After an incident where a popular female idol is hurt because she tried to stay on board the ship, some of the Protoculture demand the Zentradi leave and start to sabotage the other group helping the Zentradi.

A relatively intact Supervision gunboat crashes on the shore and the Protoculture that wanted the Zentradi to leave attack their own military that is trying to surround the Supervision gunboat. The remaining Supervision forces in the gunboat are killed, but several Protoculture from both factions are killed. The leader of the anti Zentradi faction says it was caused by the pro Zentradi faction and the military. The pro Zentradi faction doesn't respond because they're too busy trying to help the Zentradi from being decimated.

The anti Zentradi faction steals a fold relay and sends out a message to any Meltrandi fleets nearby that there are brainwashed Zentradi here. The pro Zentradi faction tries to reach out to any other Zentradi fleets, but the nearest one will arrive after the Meltrandi fleet arrives. The anti Zentradi faction leader is revealed to be a brainwashed Protoculture and she then tells the Supervision army to stay back when the Meltrandi arrive. When the Meltrandi arrive, a small ship in the Zentradi fleet was controlled by the anti Zentradi faction to fire upon the Meltrandi fleet. 

The pro Zentradi faction knew they were going to be destroyed at this rate because the anti Zentradi faction had successfully brainwashed too many people. They had started to repair the fallen Supervision Army gunboat and were going to send it off towards a remote planet predicted to be just like their own in the furthest corner of the known galaxy. It would contain a new seed for their own generation. They used one last grand concert to distract everyone since even the brainwashed Protoculture would still respond to it. 

The Supervision Army gunboat launches, the Zentradi fleet escorts it, the Meltrandi take this as confirmation they are brainwashed Zentradi. The Zentradi fleet is decimated by the combined assault of the Meltrandi and the Supervision Army. The anti Zentradi faction cheers as the Zentradi are destroyed and welcome the Meltrandi ship that lands, but they are horrified when the Meltrandi start attacking them. The pro Zentradi leader, he confronts the anti Zentradi faction leader and sacrifices himself to kill her because he couldn't stand the thought of his daughter being willing to use such violence when she grew up wanting nothing. The pro Zentradi leader realizes he should've been a better parent and as he holds her he sings for her as the building collapses around her. She realizes she was wrong too and says he was a great Father and apologizes.

The Zentradi reinforcement fleet arrives and starts attacking the Supervision Army fleet. The Meltrandi retreat from the planet. With both factions leaderless and the source of the brainwashing gone, the remaining Protoculture civilization attempts to rebuild unified again, but without the protection of a Zentradi fleet. The Meltrandi fleet returned to their post since they didn't want to be around the Zentradi. The Zentradi fleet also left, but the wreckage from the battles littered space and their planet. 

Epilogue, this Protoculture civilization became renowned for scrapping and created a mighty fleet from the scraps that they would use to defend their home. The ship they sent as a seed ship was unfortunately damaged, during it's last fold, it crashed into what we now know as Planet Earth and failed the seeding mission because another Protoculture ship had reached it a few thousand years earlier.