I didn't know that the FBI intended to interrogate those guys in Khartoum. Of course it has also been widely reported that the Sudan offered us intelligence on bin Laden which we didn't take. I believe I have also read detailed stories of diplomatic initiatives from the Sudan around this time that the United States ignored for some reason. I'll have to go back and look at those.
Still seems quite incredible to me, though. You are certainly right that Clinton is not a stupid man, so what would his motive be?
I suspect bin Laden had been involved in dirty business with Clinton in the past. Clinton found him useful, thought he might have occasion to use him again, and feared giving him occasion to reveal what he knew. There is good reason to believe there was Middle Eastern involvement in OKC, the Ron Brown flight took off from a Bosnia infested with Islamic fighters, many of them led by Zawahiri's brother, and even the embassy bombings briefly took attention away from Monica.
That is what I suspect Clinton's motivation was.