Having a backup will allow you to test that aspect out.
Bear in mind not every Chocolatey package is an installer package, there may be some non-installed applications contained in these subfolders that could potentially go missing. You might first back up the sub-folders lib and bin just in case you find undesirable results in removing Chocolatey. Most of Chocolatey is contained in C:\ProgramData\chocolatey or whatever $env:ChocolateyInstall evaluates to. Since it is not actually installed in Programs and Features, you don't have to worry that it cluttered up your registry (however that's a different story for the applications that you installed with Chocolatey or manually).
Should you decide you don't like Chocolatey, you can uninstall it simply by removing the folder (and the environment variable(s) that it creates).
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