Um, no, not really. My main concern was to insert flotillas with minimal changes to the rules--so it's not too much trouble to simply slot in, as it were. I like your idea, however I think there should always be the possibility of taking shield and thrust damage (think of it as shrapnel from exploding flotilla ships impacting other ships).
Here's a first draft of the flotilla damage concept:
"Units designated as Flotillas should be treated as having Fragile Systems for weapon, system and munitions, but Re-inforced systems for thrust points and shields"
That gives an automatic 50% reduction in weapon, system and munition damage but a much reduced chance of thrust or shield damage, representing the reduction in raw firepower and loss of unit coherency, but showing that ships are rarely physically affected by other ships being destroyed.
