I know it's a difficult decision to make, but it sounds like it was a good one for your family.
Getting two puppies at the same time isn't recommended anyway. They both need individual socialization and training so they bond properly to you, not each other, and grow up without issues like separation anxiety. Housebreaking two puppies can be very difficult, too.
Also, since the puppies are from pet stores/puppy mills, they both may have genetic health conditions that may not show up for years. It can be extremely costly to have just one puppy mill puppy, let alone two.
Here are a couple articles that may make you feel better about your decision.
Two Puppies or One? - VeterinaryPartner.com - a VIN company! Think twice before getting 2 puppies - Pittsburgh Tribune-Review