I have watched all 3 Wick movies several times, and in all 3 movies there is never a civilian killed by Wick. That's not to say that none of them could have been killed, particularly in Wick 2 there are a lot of scenes where Wick misses his target and there are civilians in the area (that whole subway scene shows a lot of civilians in close proximity and a lot of missed targets), but none of them are shown on screen to have been hit.
Side note: as to the status of Helen, John's wife, I lifted this from the Wiki:
Bridget Moynahan as Helen Wick: The beautiful wife of John Wick.
On the character of Helen, Leitch stated, "Helen's the crux of the
movie, so to have an actress like Bridget come on board in such an
important role was gratifying. She's got an elegance that is
captivating." Leitch spoke very highly of Bridget's acting talents and
when cast in the role of John's wife she decided not to read the
screenplay, believing that the limited amount of information would
serve the story well. Moynahan stated, "There was a large portion of
the story that I didn't want to be informed about. I didn't want or
need to know that side of John. Helen brought love and light and joy
into his life. Knowing the other side of it would make it a different
story for me."  Iwanyk shared Moynahan's sentiments, adding,
"Helen probably thought John had some skeletons in his closet, but it
wasn't important. All we know as an audience is that the moment he met
her, he became a different person. Love changed him."
That remark about "skeletons in his closet" should give an impression that Helen wasn't a hitman.