Xamarin Studio is MonoDevelop with addins and Xamarin brand. See this tweet from the main developer of the project. It is open source and is in GitHub .
If you want to use Xamarin Studio without Xamarin, just disable the addins and use it as you used MonoDevelop. Everything you do in MonoDevelop, you can do in Xamarin Studio.
From MonoDevelop's download page :
For Mac and Windows, you can download Xamarin Studio, which is a MonoDevelop package with the Xamarin iOS / Android brand and plugins. Note that a Xamarin license is required only if it will develop on iOS / Android projects, all other projects are free and unrestricted.