OK, if this has become a concern, here's what I think you should do.
Stat out your evil organization - every major member has a full character sheet. List all their minions ("5 third level rogues"). List all their available cash, items, etc... Make a list of their political connections. Create a group hierarchy chart. Make notes on how each member relates to and interacts with all other members. Who is after whose position? Who has private ulterior motives for doing certain things? What is the group's long-term strategy? How are their assets deployed across the world? How many current missions and goals are going on, how important are they to the group, and who is doing them?
If you go through all this trouble, you might find that the minions and resources available for party-hunting aren't as unlimited as they appear at first. The party might be a thorn in their side, but elimination might not be a major goal if, for instance, there are several adventuring parties on their hit list, as well as several major plans nearing completion.
Then legitimately role-play the villians assigned the hunting job, according to the resources and minions at their disposal. What do they do with the limited time available to them? Where do they send their limited supply of minions? Where do they set up base and how is it protected (self preservation will be on their to-do list, which further draws away resources that might be devoted to party-killing)? What spells are prepared and cast each day, as a matter of routine?
The only thing I might avoid as a DM is the Scry-and-Fry tactic (Unless it's a tactic often abused by the party). There is a rationale for this. First, the resources devoted to party extermination might not include a caster with enough spell slots to make this viable. Second, if it is viable, it's very much an "all the eggs in one basket" strategy. If the party somehow fights them off, that's a tremendous amount of resources/minions expended that are potentially difficult or time consuming to replace. An evil villion might instead opt for a longer, more time-consuming method that keeps himself safer and doesn't run the risk of such a spectacular failure.
Great, now I'm thinking I'll have to follow this advice for my own anti-PC Evil Organization.