A good cleric (or a neutral cleric who worships a good deity) channels positive energy and can choose to deal damage to undead creatures or to heal living creatures. An evil cleric (or a neutral cleric who worships an evil deity) channels negative energy and can choose to deal damage to living creatures or to heal undead creatures. A neutral cleric of a neutral deity (or one who is not devoted to a particular deity) must choose whether she channels positive or negative energy. Once this choice is made, it cannot be reversed. This decision also determines whether the cleric can cast spontaneous cure or inflict spells (see spontaneous casting).
That sounds right to me. So if you worship a neutral deity (say Abadar or Gozreh), the cleric will pick whether they channel positive or negative energy, but a cleric of Asmodeus or Zon-Kuthon will always channel negative energy regardless of the character's alignment. Same with the good deities too.
Yup, short of homebrew there's no getting around it; if either your cleric or your deity is evil-aligned, it's negative energy for you.