"So Pakistan could have done a lot of things, and done them a lot earlier than they ended up doing (closing off supply routes, shutting down US bases, severing aid ties)."
The US leased one airfield and were, in fact, ordered to leave it by the Zardari government. As for closing off supply routes, Pakistan only has nominal control over FATA bordering Afghanistan. Last, the PPP/ANP/MQM that came to power in the aftermath of Bhutto's assassination and the uprising against Musharraf (who never complained about violations of Pakistan's sovereignty) were hostile to the Taliban and the pro-Taliban parties (chiefly the PML-N, but also the PTI and the religious parties), so weakening the Taliban helped them (at least in the short term).
So no they really couldn't have done anything to retaliate. If the US pulled the rug from under the PPP there would have been another political crisis, and Pakistan has only gotten through an electoral term one time in its entire history (and that's this recent 2008-2013 term). Pakistan is in a very weak position to do anything to the US. It took Pakistan all they could just to get from underneath the sanctions implemented against them in the aftermath of the nuclear tests of 98, which brought Pakistan to the brink of bankruptcy.
As for aid making a country more independent, that absolutely hasn't been the case with Pakistan. Aid was cut off during the '65 with India. It hurt Pakistan immensely. Aid was cut off again during the '71 war with India. It hurt Pakistan immensely. Aid suspensions in the 90s led to a financial meltdown which led to Musharraf's military coup.
By contrast, when aid was generous - as in the late 50s/early 60s and throughout the 1980s, Pakistan was America's "most allied ally".
I'd like to see the research on this.
"n fact, the current Libyan government would not exist if it were not for the US government. So based upon what you just said shouldn't they have just bowed meekly like Somalia did?"
Yes, but the Libyan government also wouldn't be in power without the fighting prowess of the LIFG, so abducting an Al Qaeda leader in Libya isn't making them any friends with the people who got them in power and who are actually can make trouble for them on the ground. This is in contrast to the government in Somalia, who is absolutely at odds with Al Shabaab.