Clark had every opportunity to open up a bit to Lana and never did till it was 'too late'. All he had to do was explain to her that he was also a 'meteor kid' and how they affected him. He could have explained that the green meteors made him ill and the red ones made him 'crazy'. It would have made life with her so much more explainable and easy for the two of them.
At the end of this same episode, she told him it would be okay, if he would be meteor affected. And throughout the whole series, there were much more moments indicating that she would understand and accept him with his secret than otherwise. But he always chickened out anyway.
Guilt made Clark keep his secret. He believed he’s responsible for Lana’s parents death. Lana needed to be a little more patient. However, I would have told her anyway.
Your comment is so slow. Lana didn't know Clark's connection to the meteor shower atp! Anyone in her place would feel this way, that meteor shower killed her parents and brought meteor freaks in their lives that often tried to kill her.
If your enemies found out that you had a true love (Lana), which is Clark's heart, they would definitely go after Lana to get to Clark. I think Clark knew that too and he didn't wanna put Lana's life in jeopardy. If something was to happen to Lana, that would crush him!! It's the same reason Peter parker kept his secret for Soo long from Mary Jane, love if his life!! If you take away a man's wife, his true love, in a way, he's never the same after that! Kinda damaged!!