Pronunciation of "xeno-"

English (and most other European languages) imported many of the Greek roots it uses a long time ago -- long enough that ordinary sound changes took place subsequently which modified the original Greek pronunciations. Just as we no longer pronounce Anglo-Saxon words the same as the Anglo-Saxons did, we no longer pronounce Ancient Greek words the same as the Ancient Greeks did. In particular the Great Vowel Shift of around 1500 CE significantly changed the way we pronounce vowels. Looking at the Greek eta έ [ɛː] vowel:

Middle English [ɛː] --> [eː] --> modern English [iː]

..giving us "ee" [iː] instead of "eh" [ɛ:] for the sound of the vowel in xenocide.

The other part of your question is covered in this Eng.SE question. Basically, many Greek roots came to English through French and then were simplified to meet English phonotactic constraints. So Gk [ks] --> Fr [gz] --> En [z].

(Interestingly enough, a similar thing happened in Greek itself, though not to ε. E.g. the letter η (eta) is now pronounced [ita], among many other changes.)

No English speaker ever says a word that begins with /ks/. This cluster can occur in certain contractions, but speakers will deny that they say it, because it is a speech contraction and they think they're saying prototype words instead of physical sounds.

The same is true for Latin, French, Italian, and pretty much all European languages that English has borrowed words from. Except Ancient Greek. From which all European languages have borrowed words, usually spelled with X, which is a letter pronounced quite variously in European languages.

Mostly they've all had to consider the /k/ silent, and then either voice the /z/ part or devoice the /s/ part. Mostly English voices it to /z/, so xeno- is pronounced /zino-/.

As to how to pronounce a Greek vowel in English, that varies with a lot of factors, like how long ago the word was borrowed, and how many sound changes it has been through since then. We call the ratio of the circumference to the radius of a circle /pai/ because the word was borrowed, with a long /i:/, straight from Greek /pi:/ before the Great Vowel Shift (GVS) that changed all the /i:/ phonemes in English to /ai/ phonemes.

If the xeno- prefix was borrowed before the GVS, its vowel should be /i/; but if it was borrowed after the GVS, it should be /ɛ/ or possibly /e/. However, as it happens, it's always pronounced /i/; so, whenever it turns out to have been borrowed, it's actually pronounced as if it was borrowed a long time ago.