Call me crazy, but I always thought that it worked like this:
Tempus and Wells traveling through time somehow upset the natural order of things.
The ship arrives early as a result.
Clark flies himself as a baby in the ship at night to attract the Kents' attention.
Things are set right again.
Clark and Lois are deposited back into their own time BEFORE Wells and Tempus can take them back in time.
Thereby making it impossible for them to have ever altered the history to begin with, since now they've never actually time traveled.
(Sort of makes the whole story pointless, but at least it was great fun to watch).
