Surely, if there is a situation where an intervention has to be made in the name of safety, and there's no easy option, then the one that preserves the positions the drivers have raced for is the correct one? For a sport, at any rate. I keep forgetting this is reality TV, though. 
One of the aims of the safety car is to deliberatley bunch the field up. This allows marshalls to have a large section of the track with no cars on it so they can clear it up. That's why lapped cars aren't released until after the track is supposedly clear, then one more lap behind the SC, then race back on. Marshalls aren't supposed to enter the track until the field is all bunched up, and if drivers start doing pit stops under the SC then that delays the procedure even more.
Personally I think they need to divide the circuit up into 5 or more sectors, impose pit lane speed limits (80kph) in sectors with safety concerns, but allow the racing to continue on other sections that are clear. You can't do that with a SC. Problem is you'd then need 2 or more medical teams in-case there was a second accident in another part of the track.
I don't see how you can devise a rule that is fair to all under all circumstances. Red Bull took a punt on pit stopping twice to put new tyres on Verstappen, and ultimatley that gamble paid off (admittedly with the help of a dodgy decision from Massi). Mercedes played the safe game and left Hamilton on old tyres twice in order to maintain track position, but came unstuck because of the timing of the Williams accident and the late SC. So 'fair' isn't achievable IMV.
However, if you write a rule book, then the rules should be stuck to.