if they were capable of making sleek weapons, and did so with the GEP and plasma, doesn't that question answer itself?
Actually, no. You're ignoring some important factors here and simplifying it to one component.
The GEP Gun and plasma rifle are indeed lethal weapons. However, their context in the world must also be considered. The GEP gun is first and foremost, a rocket launcher. Rocket launchers are usually aimed at robots, not at people. This is further illustrated through how Paul mentions that the GEP gun might be useful because there's a security bot at the statue entrance, and how your max ammo count is never high enough to use it regularly on human enemies unless they clump up together. It's also actually rather clumsy to use, especially at lower skill levels. Sure, you can make the missiles home in from afar, but the loading time for each rocket takes long and it tends to miss anything faster than a small security bot. If you're going to bring up the WP rockets, remember that those tended to burn
you most of the time you attempt to use them, so they weren't exactly elegant.
The plasma rifle is referred to many times as an experimental weapon, and so it would only make sense that the design would be more slick and futuristic than other weapons, to make it look like this grand new invention in the field of weaponry. If you do actually look at it within context though, you'll see that it tends to be as clunky as the GEP gun too, it fires slowly, the shots do splash damage that hit you at close range and they never hurt enemies for much in the base game(though the last one could be attributed to a coding mistake and thus not intentional).
So they don't refute my point.
Discouraging the player from a complex system after spending time to build it is the mark of an experienced designer... or of overtly ambitious people.
You'll see that there are many games under the "immersive sim" label where complex systems are built but are made optional.
Your points about role playing games not being about shoe horning players is exactly why Ion Storm resorted to subtle tactics rather than make it explicitly discouraged. They knew people would complain if the lethal options were actively discouraged, so they didn't do that.