I'd need to know more about the coop before I could make any kind of judgement on whether it was suitable for alpaca housing. In terms of safety of housing alpacas where chickens once lived, I don't see any problems.
It would be used as a shelter and they would have constant access to a paddock. I'm just trying to see if I could even get alpacas or if it will always be a dream. My parents say that we don't have enough room for alpacas, but I measured and we do have enough unused land for 2- 3 alpacas.