I used to have *exactly* the same problem - a huge number of yellow sheep-hybrid pians round that tree at the end of Course 2 that totally slowed the game down whenever I passed that point. Fortunately they seem to have spread out a bit now, so it isn't nearly as bad. In most levels, I seem to have reached a point where there are no pians anywhere near the "main route" I fly along, because they've been inadvertantly massacred so often that the only ones left are in out-of-the-way areas.
My answer would be: if you're planning on playing the game quite a lot in the future anyway, just murder them all and the situation should right itself in time.
As a note, I don't think that having one save game for scoring and another for breeding would work, because if I remember correctly all saves draw upon the same A-Life data (it takes up a hefty chunk of space in your Saturn's memory, which is probably why there's no option to have multiple A-Life saves). You can have a second A-Life save if you use a memory cart, though.