Magnifique DOES have an uninstall function built in. The problem is that the theme creator writes the uninstall script, and sometimes its not complete. But there are some cases in which the script is fine, but your particular setup or previous modifications may complicate things. In any case, with app mods, its hard to be perfect.
If you want to avoid risks at all, just do not install "custom mods" (leave it unchecked), and just go with the Main system (window) theme which is handled by the app and not a developer written script, so its very safe and very easy and fast to uninstall.