Weeeell ... if you were feeling particularly adventurous the TGD files are just text files ... A small tool could be written to inspect the file, list the available populations and let you enable/disable (all/one/some of) them. Then you can use the File > Revert to Saved function to re-load the file.
At least, it looks that way after a very cursory inspection ... I created a TGD with a couple of populations, opened the TGD in a text editor, changed the "enabled" value of the populator_v4 node from "1" to "0" saved the file and then used Revert to Saved in TG3and the populations were disabled in the Node Editor.
Of course, before running such a tool, you'd want to save your scene so that manual edits to the file made by the tool included the latest data and Revert to Saved would reflect them ...
Anyway ... when all you have is a hammer everything looks like a nail ... and I've been doing a lot of scripting lately, so it's the first thing I thought of.

As a matter of fact, I have most of that tool written in the form of a small TGD file inspector and value incrementor I wrote last year when there was talk of putting together references of what small, incremental changes of values looked like. I never deployed it (a couple of reasons being that it will only work on Windows and another being that I can't sign my code ... I only write for myself and I trust me but I don't expect others to!.

).
Regards,
~Micheal