interfering with genes for arbitrary purposes risks upsetting the entire balance the gene pool has developed without purpose.

Let us look at some of the history of eugenics. Humans have been practicing eugenics for 100s of years with crops and domesticated animals. The results include a much enhanced food supply (from both animals and plants), and a "partnership" with dogs that works well for humans and appears to work well for dogs.

So it looks like interfering with the gene pool for our purposes certainly shifts any "balance" the gene pool had developed without purpose, but I can't put my finger on the bad part of that without help.

I'm guessing your comment was aimed more at changes in the human gene pool. Given that 1) evolution changes the gene pool all the time (I'm not sure if this contradicts your idea of balance) and 2) changing plant and animal gene pools is something humans have been doing for 1000s of years and appears to be quite useful to humans, I'm clueless as to how you infer that all of the sudden this is going to turn in to a bad idea when we do it more deliberately to ourselves.