The GM does not need to inject his personal opinions into the game as a reason to change the RAW. That's creating a house rule for the wrong reasons. The notion that the GM "needs" to penalize the player for the player making a choice is pretty crazy to me.
If the GM really doesn't want a Librarian using a heavy weapon (which breaks NOTHING - I'll note that psychic powers are already quite a bit better than a heavy weapon; Avenger alone is superior to the heavy flamer for killing Hordes for example and the psychic threat rules in DW are ludicrously not-dangerous) he has IC options like the Watch-Captain's advice to steer players away from that choice. Taking that to the next level, i.e. creating a mechanical setback to enforce his opinion over the player's vision is heavy-handed and comes across like the GM acting like he's god of the table.
Also a Space Marine is chosen for the squad he will join because of a particular skill he possesses. So when a Librarian is picked for a squad it is because of his psychic abilities, not his versatility. An Apothecary is chosen again for his skills, hard to save a fellow marine's life when you need to be laying down covering fire. A Tactical Marine would be chosen for his ability to fill in where the squad will need him.
Every Space Marine is trained in using weapons. Every Space Marine is expected to contribute to the kill-count AND be an expert in his field if he is a super-specialist like an Apothecary, Librarian, or Techmarine.
A GM thinking "Apothecaries should never cover fire" is just enforcing the Apothecary as the D&D gimp/healbot and taking away the player's autonomy to play his character as he sees fit - as a hero in his own right who just so happens to also be a master surgeon.
Why roll and build up a Librarian if you are going to waste him sitting in the back laying down covering fire?
Cuz the player might want to do that? And it's not the GM's role to police the player's idea of fun especially when it doesn't break anything?
You are letting the rules of the book override un-commonsense. Just because the book's rules allow something doesn't mean you need to allow it as a GM, it even states this in the book. If the group wanted nothing but Heavy Weapons they all should have been Devs.
This is hella logically-fallacious.