The Slate article is loaded with hard evidence that no one has even attempted to refute. The timeline, the firewalls, the fact that Alfa Bank was the first to contact them post-rename, etc.
It isn't clear when the FBI drew their conclusions about Trump's server, and it isn't clear that they took all of those facts into account. Neither Alfa Bank nor the FBI has made any attempt to explain those events away, and the story isn't closed until someone can.
I mean, maybe it's not true. Maybe it is just some extremely unusual spam server gone awry. That explanation is possible, I suppose. But it isn't anywhere close to plausible until someone can explain away all of the technical facts pointing towards the alternative.
EDIT: And, on another note, (the chance of Trump becoming President) * (the chance that Trump has non-trivial ties to Russia) is waaaaaay to fucking high for my liking. Cross my fingers that none of that comes to pass.