Are you sure you read the book ? The nuclear strike Ryan opposes in "The Sum of All Fears" is not against the guilty party's capital, since the guilty party is not Iran in this book but a terrorist group more reminiscent of the PLO (and also since Qom, the targeted city is not the Iranian capital).
It's been 10-15 years, and I don't have a copy handy, so perhaps I've got some of the details wrong. I'll take your word for it, but it seems to me that I remember that the reason Mr. Clark and his team targets the Mullah for assassination in either that or a later novel is because the Mullah gave extensive material support to those who did the Nuke strike in Colorado. Could be wrong, if I am apologies to Mr. Clancy. But my point was that it seemed, as a plot device in a novel, a pretty weak "swap" in combat terms: one deranged Mullah for one American city, with the Americans getting the worst end of the deal.
Then again, to be fair, I keep reading his novels as they come out (along with most of his non-fiction offerings, which I really enjoy), so I must not dislike them *too* much or I'd quit reading. Not a big deal, just my .02 cents.