I actually want to present this question in two parts:
1) First of all, xenos comes from ξένος. Nevertheless, it is pronounced with "z" instead of "ks" (/ks/). How come?
2) Let's take the word "xenocide" (the killing of xenos - strangers). Should 'Xe' be pronounced as "ze" or "zee"? In popular culture, you usually see "zee" being used. But, in the context of xenocide, there is a clear connection with genocide (/ˈʤɛnəsaid/, [jen-uh-sahyd]). What should be preferred?
I always pronounced it "zee-no-cide".
For easy reference:
- I recalled a very old discussion concerning the pronunciation of a FOSS game's title, "Project Xenocide": http://www.xcomufo.com/forums/index.php?showtopic=1639
As another example, take "Xena".