Yes, if the car had enough fuel in it Vettel would have started 3d.
The situation was Lewis was different. At that time the rules did not say the car had to return to the pits, they just said the car must supply the sample after qualification had ended.
The team screwed up and under fuelled the car, they realised this and told Lewis to stop on track, this meant he didn't use up fuel getting back to the pits and would therefore be able to provide enough for a sample.
The FIA decided that McLaren deliberately ran the car low on fuel to gain an advantage and therefore disqualified Lewis. Subsequently they changed the rules to state the car must return to the pits under its own power. The irony was that when they checked Lewis's car it not only had enough for a sample but enough to cruise back to the pits too.
If a car genuinely breaks down during qualification and does not return to the pits it may not be disqualified if the team can prove it wasn't deliberate - lets say a tyre gets punctured on the in-lap, the team can say "we didn't want to block other cars or cause damage to our own" and thy are unlikely to be disqualified. This is what RBR did today, hence Vettel was allowed to start in 3rd until they discovered there was not enough fuel in the car.