If your players encounter the Light of Terra and don't immediately start planning to salvage it- even to the extent of abandoning the quest for the Dread Pearl in favour of this alternate prize- then you should actually take it as a sign that they aren't playing the right game. Go find something other than Rogue Trader to run for them, because they clearly don't have the right mindset to succeed here.
My own players did manage to salvage the LoT- that is, stop the captain suiciding it and move it to a location less likely to be found by other Rogue Traders. After the Dread Pearl (where they also realised they wouldn't be able to hold it with so many rival RTs, and instead cut a deal with the Eldar to sabotage their rivals), they returned to the LoT. Then, rather than plan to refit it as a flagship, they were sensible enough to realise just how difficult that would be and decide the potential returns weren't worth it. So they looted it of everything they could, and then towed the hulk back to Port Wander, dropping it there and asking the Imperial Navy if they wanted their ship back.
Recovering the Flagship of St. Drusus and then just giving it back to the Imperial Navy was, I ruled, worth granting the Peer and Good Reputation (Imperial Navy) talents as cheap Elite Advances. The Rogue Trader considers this far more valuable in the long run than mere wealth.
This is pretty much exactly what my players are planning to do, including the whole "let's give it to the Navy as a goodwill gift" part.
Edited by Cavgunner, 20 December 2013 - 01:05 AM.