Using JSON is a good way to go if you are not likely to want to edit the configuration file manually, but an 'old school' .INI style config file is easier to work with if you need to be able to jump in with a text editor.
I'd suggest creating a simple component with 4 methods: i) Read a config into a variable ii) Get the value of a config parameter iii) Update the value fo a config parameter iv) Write the whole config back to the file
As others have pointed out, you are going to end up updating the whole file anyway and unless the file is huge, your application performance impact is likely to be minimal.Keeping the code simple is likely to be a much greater benefit.