For most big time breeders they don't have the time to find adoptive homes for undesireable bettas. So its either cull or send to a pet store. In my opinion it is much more humane to cull a healthy fish than to let it rot in some pet store, unless you can say with 100% certainty that the fish will receive the best possible care. Some do post their fish on craigslist but I shudder to think of the type of homes they go to.
As far as the original topic...
It won't harm the pair if you interrupt the spawn but I agree with MrV with less eggs you have lowered your %s of getting good fry. For a first time breeder it may be a good idea but don't be surprised if you wind up with no fry at all.