If Romo goes down middle of the season, they aren't going to bring someone into start immediately. Either Weeden or Vaughan will start. As I said, it would depend on how he and Weeden progresses from now and then that will determine who will start. This is why I said, the reason they are keeping Vaughan on the active roster instead of PS is because they don't fully trust Weeden.
If Orton was still around, I doubt they would have kept Vaughan on the 53.
You obviously don't understand how the practice squad works.
To sign a player to the PS, he has to be placed on waivers. If he clears waivers without being claimed by another team, then you may sign him to the practice squad. At any time during the season, another team can claim him off of your PS - and he's gone. Keeping him on the 53 was the only way to ensure Vaughan stayed in Dallas.
Try to see this one more time. If Romo gets hurt, Dallas will go out and sign a veteran QB - not to start, but to back up Weeden. Jimmy Johnson did the same thing in 1993, signing Bernie Kosar off the street to take over when Troy Aikman was injured, rather than elevating Jason Garrett - who wasn't ready (neither would Vaughan be this year). Kosar had a week to learn Dallas' offense, by the way.
Weeden is the back up, and will be all season. Vaughan will not see any live action this season unless Romo and Weden are injured in the same game. Vaughan has a huge upside, but he's going to take time to develop.