Viney informed the Crows on Monday that he would be returning to Victoria to take up the newly-created role of general manager player development with Melbourne - the club he played 233 AFL games for.
The South Australian was lured back to Adelaide and the end of 2008, after spending four years in charge of the midfield at Hawthorn.
Harper said the timing of Viney's decision - weeks after most clubs have already finalised their coaching panels for next season - would make it difficult for the Crows to secure the best-possible replacement.
"We're really disappointed…we're shattered actually. Todd's a really integral part of our footy club and an integral part of our coaching staff," Harper said on Tuesday.
"It was a massive shock. I got a phone call from [coach] Neil Craig yesterday afternoon just after we finished with trade week. We were taking a deep breath and then all of a sudden we get that phone call.
"We're disappointed and shattered, but we're also understanding of the circumstances surrounding it."
Harper said Viney had made the decision to quit the Crows and return to Melbourne based on what was best for his 16-year-old son, Jack.
The Prince Alfred College student starred for South Australia at the NAB AFL Under-16 Championships in July and has already attracted the attention of the Demons, where he is eligible to be selected under the father-son rule.
Adelaide was exploring a loophole in the soon-to-be-finalised concessions for the new Greater Western Sydney team next season in a bid to snatch Viney from the Dees, but Harper said it was clear the Viney family expected Jack to play for Melbourne.
"Todd and Meagan have got a young son Jack, who is a good footy player and they're a fair way down the track of him going father-son to Melbourne," Harper said.
"If that happens he ends up in Melbourne doing Year 12 without his family and trying to play AFL footy, which is probably a recipe for disaster.
"Todd had the offer of the role and the thought was to send the whole family back there and try and get as much support for their son as they can."
Adelaide had already made several changes to its coaching panel for next year, with former assistant coach David Noble stepping into a newly-created list management role and part-time ruck coach Matthew Clarke coming onboard full time.
Viney's departure means the club is now in the market for an experienced midfield coach.
Harper said it was disappointing Adelaide wasn't able to make a play for retired skipper Simon Goodwin, who has joined Essendon as an assistant, but that the Crows would ideally like an assistant from outside the walls of West Lakes to complement the likes of former players Clarke, Mark Bickley and Ben Hart.
"Todd brought us some great experience. He's been in the caper for six years full time and there's a lot more to it than just sitting in the box on match day. We'd really like someone who is experienced - that would be a key thing for us," Harper said.
