I'd also really prefer freeform, as it would let us avoid the whole experience/power issue. Plus, I've never liked much how the 40k systems are just weighted so much (in my opinion) towards combat.
TheGlyphstone is right, a Dark Heresy character given enough XP to match what a starting level Deathwatch character will probably be able to outshine the Space Marine, especially if the player min-maxes. This can be countered, of course, with gear as an option...A Guardsman might end up with some insane stats as a veteran, but it doesn't matter if he has a BS of 70--he's still not getting much done with a lasgun, or surviving many hits with flak armor.
Also, at that point, Dark Heresy characters level off quickly. They'll outshine Deathwatch characters in the beginning, but at that XP level, they start running out of stuff to buy with XP. You can get a lot of social skills, but, that's about it, really. The Deathwatch characters will start catching up to the Dark Heresy characters and surpass them eventually.
If we decide to go system, though, how about this compromise:
Human characters DON'T get the XP needed to start on par with Space Marine characters. If I remember right...A Rank 1 Deathwatch character has the same starting XP as what it takes for a Dark Heresy Character to reach Rank 9, the difference being that Deathwatch doesn't get to spend most of that how they want to.
Give normal human character some kind of boost. Don't put them at the same level...Maybe around Rank 4, or 5? It gives them room to show that they're experienced, and have been around enough to earn the attention to be put on Malcador's mission, but they aren't going to be outshining the Space Marines at that point.