Careful about putting her on a pedestal. She was no angel. Pakistan is like Iraq, or Yugoslavia and all the other countries cobbled together by everything other than ethnicity in that there are various parts which would gladly slaughter each other. Running the place takes a firm hand.
While she was prime minister she did nothing for the rights of women and openly supported the Taliban in Afghanistan. When she was ousted on charges of corruption she fled to Switzerland and took a lot of money with her, somewhere over one billion USD. While Pakistan did not convict her on the charges, Switzerland, after doing its own investigation, convicted her of money laundering and ordered her to pay USD 11 million to Pakistan and return a necklace which she purchased worth over USD$100,000--a slap on the wrist given how much money she appears to have taken, but a conviction nevertheless. Bhutto, like just about every other leader in the world, gave contracts as favors, demanded baksheesh in return, and made a tidy sum doing so. While she likely no more corrupt than other leaders in the region, she was no better either. Thinking of her as an Eva Peron with degrees from Oxford and Harvard may not be inaccurate.
Bhutto was seen by her opponents as a tool of the western powers. Her western education and behavior was found openly offensive by the northern Pashtun. As she no longer supported the Taliban, there was no reason for the Pashtun, who saw the Taliban as their tribal brothers, to welcome her return or so much as tolerate her either. She was seen as the political stooge of the US and the UK, ready to open Pakistan to greater cultural westernization and complete subservience to the same. This is not an inaccurate view. The US did pressure Musharraf to allow her return in the guise of allowing "greater democratic freedoms" while, in actuality, they were hoping for a peaceful transition to a Bhutto government.
Musharraf's power is balanced on the head of a pin. He's too liberal for the northern Pashtun and too conservative for the westernized southerners. He maintains power via a canny manipulation of government agencies and the lack of anyone better to take his place. He allows the Pashtun to pretty much do as they please and, even if he didn't, he couldn't force them to do anything anyway. The military of Pakistan is not powerful enough to control the northern provinces. Bhutto, it was thought, would openly invite the US and other armed forces into the region to hunt al Qaeda and Taliban hiding in the Pashtun-held Pakistani region of Waziristan; something Musharraf does not (at least overtly) allow. Many Pakistanis fear a US invasion and they may be right. The US appears to have considered the invasion of Pakistan early in the war on terror, using the threat to pressure Musharraf to cooperate with the US in hunting bin Laden, al Qaeda, and the Taliban. While Musharraf is not loved, the Pashtun see him, compared to Bhutto, as the lesser of two evils.
Pakistan is a nuclear power. They have nuclear weapons and a very dicey border with neighboring India who also possesses nuclear weapons. Nuclear weapons in the hands of a Pashtun-led Taliban-style government is seen as a world security risk and all the major westernized powers realize this is the greatest potential threat to world security. Keeping Pakistan's government out of the hands of the Pashtun is essential. Bhutto taking power was seen as a way for the west to have (as much as possible) one of its own in power. Musharraf could have left in the dead of night on a plane or two with his family and retainers and slipped away to Switzerland or some other place and live happily in a villa while Bhutto was swept to power. That appears to have been the plan. The question is, did Musharraf believe that he would be allowed to get away with it? Would he be prosecuted as Bhutto was or worse, perhaps extradited to Pakistan to face charges and possible execution? The US isn't terribly kind to fallen dictators it has supported in the past. Musharraf need only have looked at the Shah, Noriega, Pinochet, and Saddam Hussein to see that former US puppets get the short end of the stick (or noose) once they were no longer of use to the US. Musharraf had no reason to believe he would be safe from Pakistani or US prosecution no matter where he went.
And that's the beauty of the assassination. Bhutto already had enemies who wanted her dead in the Pashtun. All Musharraf had to do would be to make it appear pro-Taliban/al Qaeda sympathizers assassinated her and he would be in the clear. Suicide bombing, a favored tactic of al Qaeda and other radical muslim groups, is even better since the first rule of assassination is to kill the assassin. All Musharraf needed was someone he could convince to do it, likely by threatening the lives of the assassin's family members. All fingers would point to someone other than Musharraf.
I want to see how this plays out.