Thanks for all the input on my post. For whatever its worth here is the exact scenario:
There were actually 2 big bad guys and their band of minions. They had overtaken a strategically-important lighthouse for the purpose of extinguishing the light and messing up navigation in the area. When ships would break on the nearby rocks and shoals, they would pirate the pickin's.
The PC's nearly wreck on the shoals and go off to investigate the burnt-out lighthouse while the crew of the ship repairs the crippled vessel. Big battle number one drives the bad guys and their minions out of the lighthouse proper. Big battle number two is the party pressing the attack as the bad guys stage a tactical withdrawl back to their pirate vessel hidden in a cove down the beach. Probably 80% of the minions are slain. Bad guy 1 is hurt pretty badly(maybe down to 1/4th of hps) and has expended most of his stash of potions and spell-like ablilities for the day. Bad guy 2 is essentially unharmed as it spent the majority of both battles invisible and only staged opportunistic attacks before immediately regaining invisibility. During a counter-attack by the bad guys, one party member is felled -- stabilized but helpless and now "behind enemy lines". Of the party members still on their feet, two are down to less than 25% of max hps, two are at maybe 50% hps, and one is only mildly scratched. Everyone is out of (worthwhile) spells and a ton of potions, scrolls and charges have been expended in the two battles.
The PC's parley and allow the surviving bad guys to flee with their lives and their loot in exchange for the safe return of their helpless comrade. Bad guys agree and flee the area in their ship.
I intend on having the Big Bad Guys return at some unspecified time later (when the PC's least expect it). Undoubtedly they will gain levels between now and then. But again, given this full picture, is the consensus still that full CR-based XP should be awarded now AND later? Obviously PC's will get "story award xp" for busting up this criminal enterprise, but I was just wondering about Cr-based xp.
I would love to simply go free-form XP for the entire campaign, but I deal with too many game-crunching players to do that. They love to add stuff up. Yeah, yeah, its my world and all that and I can do whatever I want as DM, but they are the audience....
Thanks again for the input and ideas!