Nice photos, and an interesting thread.
I grew up in central NY, and at the time that I lived there (through '98) coyote sightings were relatively rare (I spent ALOT of time afield and never saw one). My father owns a piece of land that for years provided us with great deer hunting opportunities; but the last two years, for the first time since the family has owned it, he didn't deer hunt there. When I asked him why, he simply said "Coyotes". When I asked him to elaborate, he described in some detail the decline of the deer herd in that area over the past several years. At first he didn't know exactly what to attribute it to, but the increased coyote activity that he was experiencing gave him a pretty good idea. One day a couple of years ago he ran into a good friend of his who is a wildlife biologist and who was studying coyotes in the area. As it turns out, his friend had been videotaping a den on the piece of property adjacent to my dad's, and he said that over the span of two months, the tape showed 41 fawns being brought back to that one den. If one den can contribute that much to fawn mortality, I could certainly see where coyotes, one they got a foothold in an area, could wreak havoc on a deer herd pretty damned quickly.
That said, I personally wouldn't kill the pups, or their mother (unless it was clear that they were at an age where they could adequately fend for themselves).