Balance-wise it'd be a case of trial and error. Just remember the relative power scales: Rogue Trader characters are likely to be more powerful than Guardsmen, who are in turn likely to be slightly more powerful (and certainly better equipped) than Acolytes.
As far as mixing them though, yeah, they all use the same rules base, with each game being a better refined rendition of the last. I'd use the Only War combat rules* over DH1.0 and Rogue Traders, just 'cause they're the latest version.
What sort of game are you setting up?
*Full Disclosure: I wrote the combat rules in
OW, but as I said, I'm recommending them because they are the newest.