I'm one of the players in question. The Assassin (Death Cult, not Vindicare) specifically.
Giving me a level 1 Dark Heresy character, and asking me to hang out with a Space Marine and a Rogue Trader and go on missions with them is ridiculous. I'd have 4 stats at 25, and a boot knife, and the Marine would have a 55 combat skill and do 1d10+23 with his chainsword. How is that even an idea? Not to mention my Rogue Trader Arch Militant (The class from RT the other player wants) has a BS of 69 at Rank 1, which means I might as well not even play if I am level 1. Again, its not just combat either, his characteristics will be higher than mine to be enough that he is better at all skills than I am, too.
Not to mentiion his untrained skills equal my trained ones. I don't want to play a space marine at any point, so I don't see what value there is to having 2 characters, unless my second character is a Kaballite Warrior. That I could work with. Space Marine? No thanks.
My thought would be to pick a combat system, like Black Crusade and use it. Then equalize xp, RT is supposedly around 8000 and Marines around 13000, so I'd give the DH characters like 9500 or so xp, and the RT's like 1500, give out reasonable gear to the RT in addition to the free aquisitions, give out whatever gear a Rank 7 DH character should expect to have,and limit the Marines gear to whatever he starts with + signature gear talents and anything he loots.
It might not be exact, but I think its close enough for both a game, and government work.