I have managed to make Sitecore 9 and Helix working together. Yaaay!
There is a feature/v9 branch of Sitecore Habitat, where habitat guys unhurriedly adjust Habitat to Sitecore 9. I would advise you to take a look at that at least. One thing to mention (as for 01-Dec-2017) - you'd need to reference all the Sitecore 9 dependencies from NuGet manually, please use *.NoReferences version of each library)
Update: I've recorded entire process of installation Helix with Sitecore 9 on a clean developer machine, that already has Visual Studio 2017, SQL Server 2016 and IIS installed. For installation process also required: PowerShell and Chocolatey. Important: all the manipulations are done as Administrator.
Hope one may find useful this 24 minutes video. Thanks for watching!