It's stupid. We have all the technology to make sure that these kind of situations don't happen but they do. Hell, the Cowboys are getting "do-overs" this year for their stadium, why can't the NFL hire 4-5 people to sit in a replay booth during games and watch every play after it happened and examine where the ball should be placed. The refs should merely be the on-field assistants to the replay booths. The booth would have constant communication to the head ref and tell him where to spot the ball at the end of the play, where to mark the first down and more. The refs would call penalties, but each penalty would be reviewed before the ref actually makes the call. i.e., Packers score touchdown but offensive interference is called on the receiver. Instead of calling the penalty like normal and enacting it the booth would watch the play, determine if there was INDISPUTABLE (key word) evidence to overturn the call on the field and let the head ref know before the final call is made. I doubt it would delay the game as replays are available so quick now. And it's not like they have to take a super close look at it, just determine if it was a good call or not. If it was obviously bad, they'd overturn it but otherwise let it stay.
Sure you can call it opening up pandora's box but if it's done right you don't have to worry about it. Like I said the technology is in place to do this. In fact, in the future I could see them putting GPS devices on the tip of each ball and have a threshold mark at the first down marker. If the balls crosses the threshold, first down no questions asked because they'll know if the ball crossed the plane and when.
All in all I don't think it's really that hard to institute and regulate. The technology is in place now and I'm sure many of the people are willing. The problem is that there's so much else on the table for league officials and owners, they can't take the time to even introduce some kind of official change. It's not like it can be changed with a snap of the fingers, they'd have to focus solely on this subject for an entire offseason, which is why I don't see anything being done about the way penalties are called now. Simply because it's too much work right now to change.