Okay I just rewatched the scene a few times. Rumple speaks to Belle-box about her dreams and then the room starts to shake. Rumple actually acknowledges what is happening: “a portal” he says. He then looks at the Belle-box, the crystal and back again at least twice if not three times. In other words, he had enough time to pick up the box and get to the crystal before the actual portal opens on the bed. He then lunges for the crystal and then looks back over to the bed where the portal opens. I think he made a deliberate decision in that moment (however he will rationalize it, he went for the crystal first after thinking about it)
For that to make sense, Rumple would have to know that someone was after Belle. At the time he didn’t know who was opening a portal but did know that it was someone who obviously had magic to do so. If we assume that magic people can “feel the aura” of the crystal why would he assume that they were after anything else. I think he looks at Belle as in deciding what should I do now, the only thing that can save her is the Crystal. He then grabs for it, looks back sees the portal take Belle and then lunges for the mattress like he can’t believe that just happened. In other words he expected the portal to take the crystal and leave Belle alone.