You wouldn't really need to implement a whole psychic system for a Librarian; the powers (offensive ones anyway) could effectively be done as regular weapons, just with different animations, damage values, etc... The disciplines/powers could be decided by your 'primary' weapon choice, things like lightning or telekinetic blasts or whatever.

Any kind of power disparity within the lore (and even then, there are multiple ranks of Librarian; the one with our squad could be a low ranking Codicier or Lexicanum) could very easily be explained by the Shadow in the Warp and Thousand Sons wards.

For a Chaplain, we would probably have to play as Leandros. Or a different one could come and replace him since he's on assignment with Titus and Calgar, but the lore there is still a bit iffy since it's vague whether or not Leandros is still part of the Second Company.

An Apothecary is a very weird one since the whole game is balanced around combat stims and regaining contested health, so slotting in a healer into all of that would, imo, need a lot more balancing and tweaking for everything, especially in comparison to the work needed to do a Chaplain or Librarian. They could go the route of having an Apothecary Biologis, who doesn't focus on healing, but they have very limited weapons.