Progress thus far:
Using the GC2ImprovementEditor, I tinkered with the Cathedral of Valor improvement. It seems that structures classified as "normal" cannot provide civ wide bonuses. When I made the CoV a "Super Project" or a "Galactic Achievement," the bonus works as intended, but that sucks because I can only build one. 
Unless someone has an idea for a workaround, here's what I'm thinking of sticking with:
Cathedral of Valor
- 400 build cost (up from 300. Still no maintenance cost.)
- +15% to Soldiering.
- Removed 33% planetary defense bonus.
Since I can only build ONE Cathedral now, I decided to futz with the space cannon too (tech available before the cathedral.)
Space Cannon
- Same build cost, but only 2 bc maintenance cost instead of 3 since I'll probably be using these on my worlds instead of the Cathedral.
- 33% Planetary Defense down from 50%
- +15% Planetary morale instead of +10%.
Does this mod seem fair? I'm going to test it out to see what I think. The only thing that bothers me is that the CoV is available so early on that it could give the Arceans an unfair early soldiering advantage. Thoughts?