Yep, I do the same thing, though with a caveat: is the threat really gone, or just delayed? Many of the NPCs from the module that got away are still out there, able (and willing?) to cause trouble. For those, I gave half XP, since they eliminated the immediate threat, but not permanently.
In fact, one of the issues they have to deal with is one of the Black Earth cultists left the cult, taking up residence in Red Larch. Over time, many lower-ranking cultists fled from the PCs, joining him in Red Larch. Now he's running the town, protecting it from other threats, bringing in creatures from the Earth Plane, building up his own power base. Is he a good guy or a bad guy? Well, that depends on if the party get in the way of his ambitions. But he's certainly not "defeated".
I think it needs to be looked at in the term of scenarios, rather than individual creatures. Did the PCs encounter the cultist and stop the threat he originally posed? Then they get full XP for defeating him. The fact that he's taken up root somewhere else and started a new plot is irrelevant to that original scenario. (And the new scenario, should the PCs resolve it, should reward full XP as well.)
Now, if there's a handful of cultists the PCs never encounter at all that decided to pull up stakes and start a new evil scheme elsewhere, then the PCs obviously wouldn't gain XP for them until they actually encounter and defeat them in their new scheme.
In general, it's best to look at each encounter as a situation that needs to be resolved. While combat is the most-common solution in D&D, stealth, diplomacy, etc are still possible options, and the XP award should be for resolving the situation.