JAKARTA, Indonesia - Al Qaeda is responsible for a series of deadly church bombings in Indonesia and plotted the assassination of President Megawati Sukarnoputri, according to the confession of a top agent from the terrorist network caught here. Omar Faruq, a Kuwaiti who described himself as Al Qaeda's senior representative in Southeast Asia, said the group hoped to trigger a religious civil war in Indonesia that would lead to the formation of a ''pure Islamic state,'' according to a confidential US document obtained yesterday by the Los Angeles Times.