I don't know that much about Putin, but "some hands in Putins rise to power" is not really substantiated by your article. It just claims that the US knew some things and didn't act on them, and provides some weak evidence for it. In general I think the hope was always that Russia would see the benefits of liberal democracy and would slowly shift in that direction. Jumping on every incident wasn't really worth it, so they were willing to forgive them. That shift to liberal democracy obviously didn't happen.

"Created Al-Qaeda" is certainly far too simplistic. There are unforeseen consequences to everything you do (or don't do). The alternative of leaving Afghanistan to their fate after the Soviet invasion also wasn't appealing. If you want to blame someone for Al Qaeda, then start with the Soviet Union and Pakistan.

These two examples also conflict by the way: in one instance they had to do more, and in the other less. It's easy to sit here in judgement decades after the fact, but at the time a lot of this was less clear.