What if the fighters at Pearl were scrambled on time?

I haven't considered that. You're right. Even if the first raid had gotten through and hit Pearl despite the US air cover, the presence of additional search planes would indeed be a very dangerous threat to the Japanese carriers. I agree that Nagumo would most likely cancel a second strike and run if he saw that US aircraft had detected his fleet. That alone would have been enough to considerably alter the historical events immediately after Pearl Harbor.