Judging from the way Petrarch speaks during the ending monologue, I've always been under the impression that the Nereid went through according to plan. He probably would have mentioned something if the node had not been sealed off. Besides, the GTVA had no way of knowing if Shivan ships were capable of surviving in the superheated gas environment of a nebula; for example, if the GTVA feared the existence of other Lucifers out there, they would have no reason to believe that the nebula would prove any deterrent. I was always under the impression that they played it safe and closed off the node according to plan. Regardless of the scientific/strategic value of studying the nebula, the risk would be too great; besides, no ship in the GTVA arsenal would be able to withstand it themselves.
As for the command animation, I seem to remember it showing the Nereid detonating while still within the subspace tunnel; when it goes up, the whole tunnel squiggles and fades away. (This could just be eyecandy, though.) There's no real canon source one way or another to suggest that collapsing a node can only occur if a ship detonates while jumping into/out of a node; just because the Lucifer and Bastion accomplished it this way doesn't mean that detonating a ship while in transit won't have the same effect. Regarding the Nereid being destroyed by the supernova, remember, the last GTVA ships had to make it through the Vega node before the Nereid could make its run. Obviously, Command was well-aware of the supernova before you escaped, so they would have to be holding off the Nereid anyway. My guess is that, after learning of the supernova, and after the last ships made it through to Vega, they stuck to plan and sent the Nereid through to eliminate any chance of the Shivans getting through.