This idea was done in Alpha Centuari, and it was fun, 95% of the time... As someone earlier mentioned, it is annoying if your going for a Conquest Victory, as not only can you not win until they are totally wiped out, but depending on how fast they can move, and how early in the game it actually is (and I've seen a race wiped out in the first 10 weeks) then it could take you ages to find them.
By which time the beggers have now got another 15 - 50 colonies, all producing ships, and you will have to fight every single one, because they won't be banded together in a fleet, oh no, because that would be too damn easy.
Then, while your concentrating on destroying the vile things, they sneak off again, or take one or more of you inner planets, and then you have two places you need to attack... Then it becomes three, because they take another couple of planets elsewhere.
The process becomes too long.... I agree it is a good idea, as long as its an option like disabling the minor races.