I like the idea of splitting the research for shipboard civilian and military labs. Maybe have the research tree go
Level 3: Civilian Evacuations
Level 4: Shipboard Labs (Weapons only; one lab per ship)
Level 5: Mobile Rulership (Requires 4 levels of Titan Research, possibly a built Titan as well)
Level 6: Shipboard Labs (Weapons and Imperial; one lab per ship)
Level 7: Stripped to the Core
Level 8: Improved Research (Cap ships count as two labs).
Another thought: when stripping a planet, the planet's health could decrease as the stripping percentage increased. When the planet is 90% stripped, a few siege frigates should be able to take it away and prevent it from exploding. Investing in the "Siege facilities" upgrade would mitigate this partially, but not completely.