Pakistani politicians and commentators can be quite colorful at times - that does not make them accurate.
The US, and various Pakistani liberal commentators, would disagree with you - in fact Indians themselves are very fond of saying that 'Pakistan ran with the hares and hunted with the hounds'.
The one issue that I would agree with you on are the drone strikes. That certainly is one thing that Pakistan should have stood upto a long time ago.
Even if your argument of 'gauging threats incorrectly' was accurate, which it isn't, your extrapolation to Pakistan's competence in handling its nuclear assets is outlandish and inapplicable. If anything, as you argue, Pakistan overestimated the threat from the US, and if it does the same in the case of its nuclear assets, that only makes them more secure. And when it comes to 'gauging threats incorrectly' the US has done that twice now with its wars in Afghanistan and Iraq, so you should be questioning US competence in controlling its nuclear arsenal before questioning Pakistan.
And what exactly could Pakistan have done to threaten the US at a time when its nuclear arsenal was just becoming operative, and it had limited delivery systems? Nuke a couple of cities in India? You really think the US would care? And what of crippling economic and trade sanctions utilizing the global sentiment against the 9/11 attacks? How would that have prevented a US invasion of Afghanistan? Not only would Pakistan have had crippling sanctions, but it would still have had to deal with the US war and invasion of Afghanistan and the associated influx of militants into Pakistan.
So given the choices, the 'bad choice' made by Musharraf was still better than the other, worse choice available.