Throwing this one out there, not that I'm particularly planning anything, just curious what your thoughts would be.

I love how comrades operate in Only War, that they're quick and easy and flex the narrative of a game without giving the GM a headache in recalculating their encounters as they're more a minor benefit. Could such a system work for Deathwatch? Each Battle-Brother taking charge of an initiate to further his training (In a Chapter game of Black Templar these could flat out be your Neophytes), and to show a larger squad of men without bogging down the numbers?

The issues I could see in a cursory glance is that the benefits might not be that much for having a Space Marine as a comrade, and that you'd need to perhaps house rule special abilities for each of the specialties much like how in Only War each job has special Comrade orders, but that can't be too hard, right?

So do you guys think it's an idea worth pursuing or is it trying to fit a square peg into a round hole?

More like trying to fit a round peg in a hole that doesn't exist. Comrades exist to provide a rule set base for something that is pretty much required in the narrative of the Imperial Guard, which is that of the nameless masses of soldiers. That obviously doesn't work for player characters, and a game can only have so many people in it or it gets bogged down, so comrades are used to fill in the gaps and round out the squad. That narrative doesn't fit the space marines at all, much less the Deathwatch.

I hate saying this because I'm always trigger happy to yell against it but in the tabletop there exists the capacity for a Kill-Team to be made up of anywhere from 5-10 members, much like a typical squadron. Now admittedly I'm oblivious to the Deathwatch fluff outside the RPG books so I'm not sure if that coincides with how large Kill-Teams can get in story, but unless you have ten players there might be a need for a squadron to be larger than there are players. Now I know you could throw NPCs into the mix but much like the point of Comrades in Only War is to minimize the bogging down with so many characters involved it could work the same way here. While I understand your point as to why the Comrade rules were created in the case of Only War I don't see too much of an issue, at least from a conceptual standpoint, why it couldn't be retroactive here. Remember in Only War each player only receives one Comrade, so assuming your group has four players that's 8 "bodies", and again it seems there's room for a Kill-Team to have that many.

But again, I'm just speaking in wishy-washy vague terms, I should probably sit down and take a closer look of the implications of the rules and their impact on a game of Deathwatch. Perhaps if players want to have a larger squad it's just best to use the Massed Combat rules.