That article would be a clinching argument in favour of the conspiracy theory, if EVERY SINGLE STATEMENT in it is not preceded with "reportedly", "it is believed", "some newspapers reported", "supposedly", "informed sources said" or "it has been claimed".
The article's writer himself seems to reasonably acknowledge the flimsiness of his speculation, but then cunningly plays right into people's paranoia by basically implying that the fact that Saeed Sheikh stopped being mentioned in connection with the money transfers after a few weeks is PROOF POSITIVE that he really was the person behind them! The sheer ludicrousness of this assertion would have been plain for all to see if the writing didn't skillfully manipulate the natural suspicion and inquisitiveness of his readers to trick them into drawing this conclusion themselves.
Their talk of "evidence" is basically some second-hand allegations made by publications as diverse as CNN, the Telegraph and Vanity Fair (seriously!), which they seem to be taking at face value even though those publications don't offer any evidence in support of them. It doesn't even look like they've checked up on them or cross-referenced it with anything else. It would at least have been easy to cross-check the dates when the FBI said the highjackers were in Dubai with the dates Saeed was there, but they don't even do that.
That article's saying that IF Sayeed and the ISI were linked to Al Qaeda, and IF the ISI had ties with the CIA, THEN 911 was a neocon conspiracy. The problem is that even if the first two speculations are true (which they don't really offer evidence for, although I personally think they are quite credible), it does not follow that the third is true! Could it not be that the CIA was unaware of the extent of the ISI's connection with Al Qaeda, or, more likely, that they were ignoring it because it served their interests to maintain ties with the ISI anyway? How does it make them co-conspirators in 911?
It's not news to anyone that Pakistan has a lot of Islamic extremists in it, and I'm not surprised that militants have achieved senior government/intelligence positions. And if you didn't know that the CIA had links to Islamic militants you're about 20 years behind. Does this PROVE (not suggest, not imply, but prove!) that the US government would have conspired with Al Qaeda in a plot to bring down the towers and precipitate an invasion of Afghanistan?