I’m not sure about the active plugin on a file part, but you can quickly go in and remove plugins that are installed by opening the Command Pallete (Cmd-Shift-P on Mac) and typing remove if you have Package Control installed.
You will see Package Control: Remove Package**
Once the list of installed plugins shows up you can click these and remove them and then test out your code.
You can do the reverse and quickly re-install the packages if something you needed was missing.
You probably already knew this so I am not sure that this will be helpful or not.
BTW: Sublime Text 3 Beta just came out and is available to licensed users. I have not done much with it yet, but it loads almost instantly.