:/ I think you're jumping the gun a bit here. It doesn't show Nyasu going in the Pokeball, just that Iris attempts to capture him. It doesn't mean he will be captured at all.

As for the shipping, tbh I don't think most of us expect any shipping out of it. They always treated Nyasu different than they did each other. He was their friend, yes, but remember that he was fired so he might have fucked something up, we don't know on what grounds he is being dismissed.

I highly doubt any of this is permanent. We just have to watch the episodes and see what happens, then go from there.