Scavenging some of the light weapons from the station could be good for a significant upgrade, those point defence thingies are awesome and the short range guns are pretty good at what they do too. Of course it wouldn't give you any more in the way of a main gun, and it is difficult to resist having one defining feature that nothing wants to stand in front of...
A constant firing laser might not fit thematically but otherwise I imagine that it would be fine, the damage would be up to Sensei though, if it is the only component on the ship then it might even have a higher damage rating then a normal laser...
My sabot cannons seem to have been replaced with beamers, I am not certain why exactly, it may be that they are overpowered against large ships or it may be that they are under powered and are difficult to improve. Whatever you do, Sensei will probably go over it and balance the thing, so being over-powered isn't really an issue, size, number of weapons, and components are a bigger deal. Chances are that if it has 20 deflectors or a single outer component with an aegis deflector in the middle of it, or its entire armament behind a couple of dozen layers of small components then it may be an issue. But if you are just asking whether or not you will be able can play if you submit a ship with a sabot cannon with 15 damage that can fire a dozen times before the first round has left the barrel and doesn't need to reload for 5 minutes then rest assured that it will be toned down but you will still get you ship...
For an example this is more or less the ship I sent in, though I did move the booster.
And this is what I have now, although that was a while back, it may have been further modified since then.
So it gains some armour around the core, the weapon pod was shifted back, the sabot cannons were replaced with beamers, and a couple of engines were installed. Sending in a super gun can and will be changed, sending in a 5000 piece behemoth might be more trouble than it is worth.
"So... We're pirates, occupying a government facility, orbiting an active colony, in the midst of what may be open war..."
*Checks that the FTL drive is working properly and ready to go on short notice...*