The three Warhammer 40k RPGs (Dark Heresy, Rogue Trader, Deathwatch) share a somewhat common ruleset, and I believe this question applies to all three.
Can I move through an ally in combat?
I'd just treat it as a dodge roll to get by, at the better character's dodge, and count it as 2 squares instead of 1.
Looking in Deathwatch, I can find nothing to indicate otherwise. However, if one wanted to be thoroughly pedantic, one could declare engagement on the friend, and then disengage, making it a half-move or move followed by a disengage (which includes a half-move).
The following response was from Mack Martin of Fantasy Flight Games:
Not a firm answer, but it will have to do.