I tend to agree with the sentiment of giving the players a small non-warp capable ship like a guncutter or the shuttle from Innocence proves nothing. But the lack of immediate interstellar travel is one of the things that contributes to Dark Heresy's pulp espionage feeling. Look at campaign setting like Call of Cthulhu or Indiana Jones. Part of the character's adventure is transitioning from one location to the other. The characters should have adventures enroute, although probably minor adventures like the acolyte cell in the Dark Heresy novels that lost their equipment to thieves. Or you could perhaps use a smaller warp capable vessel. Perhaps your players are working for a Ordos Xenos Radical who is using a recovered micro warpship that is controlled by an Abominable Intelligence. That could make things very interesting.
Salcor