Actually, I haven't found xenocide listed as a normal word in any dictionary. It is the title of a novel by Orson Scott Card, in which it is used as a word.
So let's look at another, more common word with the prefix xeno-: xenophobia. Onelook Dictionary Search reveals that the vowel can be pronounced either /ɛ/ or /iː/.
This kind of variation in vowel length is actually common for many combining forms taken from Greek. There are some contexts where vowel letters are almost always pronounced short (before a doubled consonant or a consonant cluster that can't start a word) and some contexts where they are almost always pronounced long (before a single consonant followed by a silent e), but there are also contexts where there is no clear rule.
Unfortunately, there is no general rule for the length of vowels before a single consonant followed by the linking vowel o. They may be either short or long, depending on multiple factors such as which vowel letter it is, what the etymological vowel was in Classical languages, and which specific word you're looking at.
The pronunciation of the letter e in this context may be influenced by etymology according to the following principle: roots with a short vowel in Classical languages (such as Greek ε or Latin ĕ) tend to be pronounced in English with short e /ɛ/, while roots with a long vowel in Classical languages (such as Greek η or Latin ē) or with a diphthong (such as Greek αι, οι, Latin ae, oe) tend to be pronounced in English with long e /iː/.
Here are the combining forms I've found that are pronounced according to this principle:
Long e: eco-, feto-, kineto-, magneto-, meco-, spheno-, thero-
Short e: necro-, steno-
There are nearly as many possible exceptions to this principle as there are roots that follow it. The one definite exception: the root stetho- in stethoscope comes from Greek στηθο, with a long vowel, but it seems to be universally pronounced with short e. All of the other exceptions I've found consist of roots that had a short vowel in Classical languages and show variation between short and long pronunciations in modern English: astheno-, cteno-, geno-, meso-, telo-, and xeno-.
The Oxford English Dictionary has a note mentioning this variation in its entry for meso-:
N.E.D. (1906) gives only the pronunciation (me·so) /ˈmesoʊ/ . Variants
in which the first syllable is pronounced with a long vowel appear to
represent spelling pronunciations, rather than the outcome of any
regular phonetic development. They are first explicitly recorded in
dictionaries of the first half of the twentieth century, although the
absence of earlier evidence may perhaps reflect conservatism motivated
by an awareness of the short vowel in the classical Greek etymon.
For most of the other roots I mentioned, the Oxford English Dictionary seems to prefer forms with /ɛ/: it only lists /ˈzɛnəʊ/ for the pronunciation of xeno-. So apparently this is the more conservative pronunciation. It's a matter of opinion whether this makes it more preferable.
Xena is different. For one thing, it's a name, so the pronunciation is more fixed than for most words. The pronunciation that was used in the television series seems to have been /ˈziː.nə/, and it would be unusual to deviate from this even if you pronounce xenophobia with /ɛ/.
The other way Xena is different is the morpho-phonological context. The root here is not before the linking vowel -o-, but before a Classical inflectional suffix, -a (according to Wikipedia, the name is adapted from the feminine form of the Greek adjective ξένος). In this context, a vowel followed by a single consonant is often lengthened: even people who pronounce genotype as /ˈdʒɛnəˌtaɪp/ pronounce genus as /ˈdʒiːnəs/.