There are several plausible explanations. The reasoning behind the post-event timeline is actually irrelevant.
What IS relevant to this discussion is the harrowing truth, that AQ Khan gave Tehran an opportunity on a silver platter. As we speak, had Tehran used that advantage correctly over a decade ago, then Iran would be a mature nuclear armed nation state by now. I'm not 100% sure what the outcome of that would be for Pakistan (Tehran has, at times, been hostile to us), but for Iranian interests, that would have been a massive win. In that alternate timeline, Iran would certainly not be getting bullied by the pariah state today.
Yet, you refer to this man as a "criminal".
I am beginning to think Iran will get through all this, with resilience and determination. When the dust settles some months from now, your senior most people may look back at certain points in recent history and ask the same questions being asked today in this thread. AQ Khan was the polar opposite of a "criminal". He was very much a servant of the people.
It us worth noting that Israel makes a big deal of hunting down scientists before they get to realise the fruits of their hard labour. They truly understand the importance of these men and women for a nation's security.