I think you need to think about what you mean by removing flux.
In Starsector, flux basically represents "waste energy" or "excess heat", basically, something that's undesirable. You start with zero, and as you use your weapons to do damage or use shields to absorb damage, you build up this quantity, until you max it out, at which point you need to back off or start taking damage to your ship.
By contrast, in a game like Star Control, you start with a full amount of "fuel", which you use up as you fire your weapons. In this case the more you have, the better. Star Control didn't have shields, but it's easy to imagine that you could implement shields in Star Control just by having it take away some of your fuel when it absorbs damage (the shields using your fuel to power it).
So if your objection to flux is that you don't like the idea of "waste energy" or "excess heat" that a ship wants to get rid of, it should be pretty straightforward to mod Starsector (assuming you can modify the UI; I don't know how easy or hard it is to do that) to convert it to a concept like "fuel" or "energy" instead: You start with a full energy bar, and that bar decreases when you fire weapons or use your shields to absorb damage, and then you have to wait to regain energy (just like how you have to wait for flux levels to decrease). The conversion is, very simply, just "energy = max flux - current flux". It's a very straightforward change because only the player-facing UI needs to change, and all the game's underlying mechanics stay the same.
If your objection to flux is that you don't like the concept that different weapons cost different "things" (energy, flux, whatever) to use, and that you also use those "things" to deflect enemy ships' weapons, then you might have to explain why you feel this way. After all, this concept (or a related concept) has been central to this genre of game since Star Control and probably before. (I think Spacewar also had a similar system right? I haven't played it in a while...) Flux is really the same thing, but dressed up as a negative quantity to minimize that increases when you attack, rather than a positive quantity to maximize that decreases when you attack.