The Alcubierre drive gets rid of that issue, as far as I understand, with the warp bubble theory.
Quote:
"Researchers from the University of Sydney have done some advanced crunching of numbers regarding the effects of FTL space travel via Alcubierre drive, taking into consideration the many types of cosmic particles that would be encountered along the way. Space is not just an empty void between point A and point B… rather, it's full of particles that have mass (as well as some that do not.) What the research team — led by Brendan McMonigal, Geraint Lewis, and Philip O'Byrne — has found is that these particles can get "swept up" into the warp bubble and focused into regions before and behind the ship, as well as within the warp bubble itself."
Of course, this creates a problem when you stop moving at FTL speeds...
Quote:
"When the Alcubierre-driven ship decelerates from superluminal speed, the particles its bubble has gathered are released in energetic outbursts. In the case of forward-facing particles the outburst can be very energetic — enough to destroy anyone at the destination directly in front of the ship."
http://www.universetoday.com/93882/warp-drives-may-come-with-a-killer-downside/#ixzz34HJTDkWl