Logic would suggest.
Al Qaeda are the heros of conservative muslims. Pakistan is overflowing with such sympathizers. Bhutto was a woman running for top political office. We all know how Al Qaeda/Taliban types feel about women. It's common knowledge that Pakistan's intelligence agencies/military have large numbers of personnel who are in league with Al Qaeda/Taliban types. They also know that killing her would set into motion events thats could lead to chaos. Chaos is the environment in which they operate best.
My money is on Islamic militants...aka Al Qaeda.