Well, the only reason I'm suggesting a system of some kind is give a degree of uncertainity over things like combat. Similarly, for someone who has appropriate skills (in character) but may not be as familiar with the 40k universe, a skill check lets the GM feed them the info they have, or would know.
Looking at the character sheets in the book, each class starts with a set of skills and talents. I'd think taking that as a starting point would work, and allow people to choose a few others, or swap around some.
Starting gear is going to be fun, because Rogue Traders tend to be INSANELY rich and/or well connected. You want a mastercrafted bolter? Not a problem. How about some xenos toys instead? A shuriken catapult maybe, or tau pulse rifle. Needlers, neuro disruptors, graviton guns, all available, and nothing but the best. Jokaero digital weapons, powerfists ... I think anything short of power armour seems to be available, and with the right implants you could probably get that too.