The thing is, buying that one Betta from the pet store doesn't make the store money. Buying the Betta's tank and supplies makes them money. That's why they have them, and any other small animal... so you'll buy the kits and supplies :) So go ahead and buy him and don't feel guilty, just don't support the store by buying all his stuff there if you feel bad about supporting them :)
As for breeder vs petstore for owning? Either way is fine for pet only. I personally would never breed a pet store Betta because you have no idea about genetics of them or what they will really produce.