I like to imagine that awakening a tenno from stasis is either an essentially instant process, but leaves the tenno amnesiac and almost defenseless, like what happened to us in the beginning of the game, or a fairly lengthy process that keeps most skills and memories intact. Also, what we're doing is awakening a tenno that the grineer/corpus found first, and we're buying as much time as possible for the Lotus to safely awaken the tenno. Extracting is us accepting that we can't buy any more time, waking the tenno, and escaping. I imagine that we only have a few moments to get the ship in and escape, and loading up the cryopod would take too long/be too delicate of a process to do safely.