A fool's errand perhaps, and to reconfirm my foolishness I made a couple of stabs at coining a new word myself.
The first was an attempted derivation from the Greek words for 'discovery' (ανακάλυψη, at least in modern Gk.) and 'pain' (άλγος):
AnakalgiaBut a couple of people who know a lot more Greek than I do (not hard) say this won't work at all.
The second may be more promising. Remembering Mark Twain's comments on the German language I proposed:
WunderentdeckungverlustschmerzMy German may be better than my Greek, but not by much and anyway it's still...German. I can't see something like this being adopted in English as have, say, Angst and Schadenfreude.
The poet Danae Daska wonders about a straight transliteration of the Greek word Θνησιγένεια: Thnisigenia.
This comes, she explains, from the words Θνητός (mortal, dead) and γέννησις (genesis, birth), and refers to something that was born to die instantly:
Nowadays thnisigenia is used more for ideas than for babies or other creatures, but it crossed my mind that it could work here because both the knowledge of the animal's existence and the feeling of wonder are born to instantly die by the immediate knowledge of the animal's extinction.The nearest English equivalent is probably 'stillborn.' Thnisigenia, though, could be used to mean 'stillborn in the mind'.
That still doesn't quite get us to a feeling. So how about:
wonder stillbornBetter, perhaps, except that it's a phrase not a word and it misses the idea that the animals are being driven to extinction (by human actions). More accurate would be:
wonder murdered It looks like we're not quite there yet...assuming there is a 'there'.
Perhaps the poet Mario Petrucci is right to say, half jokingly: how about just 'folly' [to describe the destruction wrought by humans on other species]? 
Another poet, working in the Scottish Highlands at present, says she thinks she has a word for it...
And perhaps other languages come close. Bengali, Chinese, Japanese, Yiddish...?
 For some reason this recalls "Macbeth hath murdered sleep..."
 I answered, "OK so The March of Folly led straight into The Age of Stupid."