Yes, I am on the same page with all of this.

Orbital bombardment is indeed a huge danger. The only solution against it that I can think of is to keep hostile ships from getting close enough to aim guns with unguided projectiles against specific targets. Which probably makes orbital defense platforms insufficient. Guided missiles would be able to hit, but they are also much easier to shot down. I guess missile defense would be the primary function of orbital defenses.
Guns in space have unlimited range, so even with very big guns you can't hit targets before they are in range to shot you. But bigger guns can also mean shooting projectiles at higher speed. Higher speed means faster arrival at the target, which means less time to evade it. So defense stations should be outfitted with huge guns that have higher hit rates at long range. (Accuracy and precision don't really apply here.) At the same time, being effectively stationary in fixed orbits, makes it easier to hit the stations from long range, as you know where they will be when the projectile arrives. Which means they need massive armor that can take hits from ship cannons.
There's probably a huge rabbit hole of physics here, which isn't worth to go into, but the general principles are something to consider going forward with this.

I believe there are forms of fusion engines where the fusion fuel is also the propellant. Those would mean only a single fuel is needed for propulsion and power, which is nice.
Not sure how much of an issue the exhausts of ships would be in engagements out in space, but ships going full throttle as they depart a station would be a massive danger. Not sure what to make of this piece of information, but I am actually inclined to just not mention it to anyone and ignore it.

For fuel stations, I think the most efficient way would be to have mines, refineries, and depots all in a single place. These stations could be the only installations in several systems, which in turn only exist on the star charts because a refueling station is needed for the route between two other systems. Of course, stations that can refuel capital ships without landing capabilities would have to be in open space, where obviously there is nothing to use as fuel. So the refueling station would have to be in orbit while the refinery is on a planet surface. That still means you need to have tankers going back and forth between the refinery and the station. And if you bring the rocket equation into this, this is going to get expensive. I guess it would make sense to have the mining and refining done on as small as possible bodies, so the tankers still have fuel left to deliver once they get into orbit.

In the end, there's one big question that really matters, and that is how many units of fuel are needed to cover which amounts of distance, and how much that fuel costs. I think fuel costs are a great element to make money matter to PCs, to cause debts, and encourage crimes or other risky jobs. But it really shouldn't become an accounting minigame. I think this is something to keep off until I have a better idea of what the campaign map will look like.