I persoanlly would like to see Chaplains as a Deathwatch class and I don't think their is a reason to miss them.
Most Deathwatch personal are selected for the role either by Chapter or other Deathwatch. I am sure that when the Deathwatch a Chaplian they would draft from a chapter who presents an orthodox or middle ground view or they an individual who is able to ratify all the disperate "cults" of the Astartes.
Its the same as with Priest irl, some might be staunch traditionalists but their is a growing number out their who recognise that if their religion is valid perhaps all religions are valid so they take on a more relaxed stance.
It would mean of course that some chapters would never provided Chaplians to the Deathwatch (i.e. the Black Templars) but lots of those chapters would be carefully scrutinzied anyway before entry as often their wide beliefs would make it difficult for thier Marines to even work with other chapters.
As an aside iirc while he wasn't a Chaplain in position in the first CS Goto Deathwatch book thier was a Black Templar who essentially filled the role of Chaplain for the DW Kill Team exposing the virtues of the Emperor and acting as religious council for the other DW Marines despite some of them being Psykers.
I would also like to see Veteran Scouts... or maybe the Astartes Scouts that some chapters (like the Wolves) field, full battle brothers who have mastery infiltration as thier means of For the Emperoring.