Yeah, any time you pursue violent action against someone that's not an active threat, that's grounds for the PC gaining Conflict.
When Luke blew up the Death Star, he was protecting innocent on Yavin 4 that were being targeted by the DS.
However, when Wedge Antilles/Lando blew up the 2nd Death Star, the DS was not a threat at that point to no one - the rebels did attack the Imperials at Endor in contrast to Yavin 4. Would Wedge/Lando get 5 millions Conflict points if they were FS?
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Nope, because the DS2 had been actively targeting Rebel ships, and the people on board knew exactly what the station was, and the station itself was a major threat to the galaxy at large. And in the novelization, the Moff in charge was getting ready to target and blow up Endor on the Emperor's orders as a final act of spite.