Xar said:
Also, if I wanted to kill them all then I could easily do that, but it wouldn't be realistic. When did it last happen to good PC's that they were systematically hunted down by high-level evil NPC's just because they foiled some of their plans or killed some of the evil organisations members?...
Oh, about two years ago, in one of our groups' 2nd edition campaigns.
Remember that, good or bad, PC's who partake in actions that thwart the plans of their opposition will attract attention from that opposition. Unless the PC's are remarkably thorough in killing all witnesses, using non-detection 24/7, and leaving no clues after the fact, they are going to be found out by those who oppose their philosophies. (Let's face it, have EVER seen a party that left no trace of their activites?)
In our campaign, a very powerful lich, a powerful priestess, and a very powerful priest had been thwarted many many times by the PC's. They decided enough was enough, they contacted one another through emmisarries off-screen, and got together to form a plan to take out the PC's one at a time. In the end, they were thwarted, but the players were sweating bullets the whole time because of the fact that some of their key NPC's and in one case ONE OF THEIR OWN went missing.
(I roleplayed the encounter off to the side with the player, and when he was captured, he was under secrecy not to reveal to the other players what had happened! He had a scared look on his face the whole time, desperately waiting for the group to find out what happened to him!!! I loved every minute of it!

)
In closing, I suggest that it would be realistic if the big bad guys of a campaign DIDN'T take an interest in PC's who were becoming terrors to their operations. So if your PC's are using evil means to solve their problems, eventually, the good guys of the realm are going to come calling, and it doesn't take a squad of 15th level paladins to take care of things - as PCat said, only a few competent guys and a battle plan.