[spoilers] Crimes against science — what can be done to reduce them
Portals: Orion's Arm is a hard SciFi setting and they have collected some theoretical physics references on their wiki that explain why wormhole portals are not provably impossible. Maybe some of this could be declared canon in Bussard.
Collisions: well, the space is large and empty, and no, planets are not that big. So for planets we could just declare that the planet image covers its sphere of municipal jurisdiction and the planet is actually small part in the middle. I dunno, maybe the orbits with the pericenter smaller than the planet's true radius could be eventually prohibited. Or the acceleration cap could be replaced by CAS-assisted atmosphere bounces for planets.
Refueling and thrust are the same issue — the in-universe time is too fast w.r.t. the player actions for the physics to be plausible. Can be solved by rescaling after the orbital mechanics is fixed.
Hidden Fun Stuff / CDI. Are you sure you want this? The drawback is that this is 1) unfixable in-universe except by declaring it was all in a simulation (the reveal being that in-universe you are just a person playing a computer game with a simulated universe, talk about breaking the fourth wall) 2) gives a game a very definite end. I think that with all this scripting etc. the game could be quite open-ended (you have achieved some plot objectives but there are many fun sandbox activities to do, like colonizing new systems or something), the in-universe official CDI more or less prevents you from having a sequel and devalues anything that can be done in the sandbox. It's the same thing, though — if the endgame sandbox is large enough, maybe people could build new worlds that merit inclusion in the updated versions.