As far as scarred ships and squadrons not heing eliminated upon destruction... I see two options; You can forbid players from adding ships after fleet creation, or you can have ships be permanently destroyed. RitR's upgrade system doesn't really have a way to add ships, so destroying ships had to go.
Adding multiple tiers of scarred seems like a better choice if you want to house rule, but it would also bring back some of the Correlian Conflict's snowball effect.