There is no proof that Lapu- Lapu killed Magellan. Actually, according to my research, he was attacked by random natives. He was hit in the arm by a bamboo spear and got wounded on the left leg. There is no name of the natives who hit and wounded him. Lapu- Lapu only led the revolt.
Lapu- Lapu led the revolt against Magellan since they don't want to be colonized by spaniards; espeacially influenced by their religion.