The argument given in defense of the NASCAR official is that they are required to take action, if possible, to prevent possible safety violations that could cause accidents or injuries to other drivers, crew members, etc.
So, since a tire rolling across pit row poses a safety threat, the NASCAR official was following the rules in stopping it. I do think, however, Johnson could have been assessed a penalty -- this was at NASCAR's discretion, but since the tire clearly would have kept rolling (the crew member whose job was to stop it had tripped and fell), I don't see how Johnson escaped penalty. It's poor judgment calls and an unwritten rule book that keep getting NASCAR in trouble.
My personal opinion: Yes, the official should have stopped the tire and, yes, JJ should have served another pass-through penalty. If NASCAR wants to avoid charges of favoritism, they better either publish a rulebook or show some consistency in their penalties.