It seems .NET Core is switching from project.json to use .csproj and MSBuild. That may be available in .NET Core 1.1 or similar. At that time it may be possible to use MSBuild to build projects and have SonarQube pick that up.
See: https://blogs.msdn.microsoft.com/dotnet/2016/05/23/changes-to-project-json/
Whether that be a good thing or not remains to be seen I guess.
Also see this link for a possible workaround to use MSBuild to build .NET Core projects in the meantime (I have not tested it yet): https://learn.microsoft.com/en-us/dotnet/articles/core/tutorials/target-dotnetcore-with-msbuild
The .NET Core tooling is going to move from project.json to MSBuild based projects. We expect the first version of the .NET Core tools that use MSBuild to ship along with the next version of Visual Studio. However, it is possible to use MSBuild for .NET Core projects today, and this page shows how.