I was in the middle of writing a post about how this didn't feel like it had a place in the game when inspiration struck for a possible solution. It didn't pan out, but it led me to another idea that I think might work.
Anyway, the idea is that sergeants will drop an "energy adapter" once you get the assault rifle. This'll give you a way to use the energy cells they drop before you get the pulse rifle, and also give an explanation for why the fuck they shoot red plasma from ordinary rifles. I'd also change cyborg projectiles to cyan, since they visually have real pulse rifles, so everything would finally be nice and consistent.