For what little its might add to the discussion regarding the autonomy of the Deathwatch, I read some random bit of fluff today from the old Inquisitor line. It said that deathwatch teams were mostly under the command of Ordo Xeno's inquisitors, but in some circumstances, an individual squad or war-band would be permanently put under the command of a marine with the rank of captain or higher. This was the origin of the Brother Captain Stern model, who stood in as an Inquisitor and leader of his own warband/band of acolytes. It also talks about him ordering an exterminatus by cyclonic torpedo bombardment. If he's not an Inquisitor, then it is by name only.
I don'tt usually cite fluff as precedent for a certain interpretation of the setting, but I thought this little nugget might Illuminate the above discussion. For what its worth, I don't think Marines should be Inquisitors, as they have enough on their plate already and they are furthermore not entirely trusted by the Inquisition (or entirely human, for that matter). But if one wanted a Deathwatch Inquisitor to be a Brother Captain, it would seem there is some precedent.
I think a metallic-looking null-box with a lock and key would make for a very attractive CE. It would be heavily built and with rivets along the seams. It would also have the deathwatch symbol stamped on the front. The leather rule-book within should be textured like stitched-together xeno-hides.