Hi @vasilli. For now at least, there will be no in-built commenting system (see thread here: Native comments system)
As the creator of Cove, I have no plans to shut it down any time soon. I love the Ghost ecosystem and being able to contribute with a small tool like this. If Ghost does create a native commenting system in the future, I will make sure there is an easy way to migrate your comments, no problem.
(If it helps, one of the Ghost co-founders is using Cove on their site at the moment.)