They can say it was because it slowed the story down, but they could have easily cut down the number of shots for the separation to make it quick.
Hell, they could have skipped the sequence altogether if necessary, starting the prep before a commercial and coming back in with the separation done and a log entry filling in the blanks. TV is filled with shortcuts. The whole reason for the transporter back in the day was to "keep from having to film the ship landing every week." Well, the same shortcuts could have been done there too, you don't always have to see the whole complex and expensive landing sequence, so I never quite bought that.
The third season of Lost in Space got around it.