Are there any real issues with using the Black Crusade rules instead of the Deathwatch ones?

I use a hybrid.

It's worked well so far, just taken some getting used to. Definitely gives more of a challenge in some areas (new autofire rules), and streamlining in others (Toxic and Concussive come to mind,a s well as Swift/Lightning attack rules).

I do much the same thing and find it a relatively easy fit to move to black crusade and it makes for a better game.

The only bit that requires a lot of work would be if you wanted to move the deathwatch psychic powers across to fit the style of the black crusade powers, but that's down to personal preference (and of course whether anyone in your group wants to be a Librarian).