Wasn't it an ongoing thematic thread in the first season, once Clark realized that his arrival coincided with the Langs' deaths? I seem to recall a big reason for keeping his secret from her was that he feared that she would blame him. At least that's about the only impression I retain from the Green Pendant Days.
She was carrying that baggage so hard, she was wearing her parents' deaths around her neck. He was terrified of her finding out, as I recall.
Not to say he should bear any responsibility for the event, though.
I watched the first two seasons on dvd recently and I didn't pick up on that, although I was kinda spacey (now that's an ironic and punny thing to say unintentionally.) trying to absorb all that shit in just three days.
I saw again the alternate present where Supergirl is head of Domestic Security working for... Fuck Kal El is thick, he was even told that that world was not real that "Jor-El" was just spinning fear like FOX to beat Clark into submission with the worst shit the "AI nanny cam who pretends to be his father" could imagine... But there was still a meteor strike even without Clarks Ship, that just kara's ship brought all that radio active bullshit raining down on smalville by itself and what was that about her mission being to find and kill baby Kal-El? "Jor-El" just loves a good wheeze... But she went as far as to say that she had been raised along side Lex (without aging in the last 20 years/but still found under the damn) and that he had protected her secret...
SHE WAS THE PERSON WHOSE JOB IT WAS TO HUNT HERSELF (Dexter much?) DOWN AND SHE COULDN'T LOCATE THE IRONY OR THE HUMOUR IN HER SITUATION STILL CRAVENLY BEGGING FOR SECURITY FROM PRESIDENT LUTHOR WHO PLAYED HER LIKE A FIDDLE... No, really for the ham fisted skill that imaginary Lex luthor displayed, he played her like a slide whistle.
I love how angry the ineptitude of this story telling makes me feel. It makes me feel like the Hulk or Lewis black.