Which is the best one? (and it being "railroady" is not a problem, I'm looking at running a one shot/marathon single session)

Are there better ones from DH or RT which could be easily adapted?

Both Final Sanction and Oblivions Edge look fairly good, and are designed for lower level characters. But they aren't one shot by design, each would take about 12 hours to finish. You could shorten them of course, but you would be cutting out some really cool stuff.

The Emperor Protects has some decent missions as well, same problem as above though.

12 hours is just about right. What books are these adventures in?

Final Sanction and Oblivions Edge are both free adventures you can find in the support section for Deathwatch. The Emperor Protects is an entire Deathwatch supplement devoted to adventures, it can be found in the products section. And I think there is a short mission in the back of the Deathwatch book too.

The free adventure for Black Crusade, "Broken Chains", can be easily adapted for Deathwatch as well.

The players won't start the game as prisoners, of course. Instead, they will just wake up from a cryonic stasis (They have been sent in cryonic stasis because of a very, very long warp-trip through half of the galaxy).