Xenophobia isn't only possible background of fanatic purifier.
What are possible reasons for unlimited extermination policy?
Racism (xenophobia)? Yes, but also:
- Religion (Spiritual background) - You are purifying entire worlds of infidels, not intending to convert anyone (Heretics of Dune, Dune Chapterhouse - core classics of SciFi genre). Race doesn't matter
- Rulers will (authoritarian background) - Leader/Governament order destroying world or even entire race for pure power projection (Star Wars, LEXX, WH:40000)
- Expansion (materialism background) - Specific race is technologically superior and find other races as useless obstacles is their patch to power. They are removing such obstacles because of pragmatic reasons, and purification-on-sight is considered as most efficient procedure (Unicron, Borg and... Time Lords, before Galifrey Fall)
Thing I really hate is lack of imagination - especially when good examples are at hand.