The latest Gnome Tweak Tool from GIT supports switching GNOME Shell extensions on / off (well, the new feature was added about 2 weeks ago but I've somehow missed it) with a click. Tweak Tool also got an option to install GNOME Shell extensions, but it was later disabled because it's too unstable for now.
For those not familiar with GNOME Tweak Tool: this is an application especially designed for GNOME 3 that lets you change GTK, window and icon theme, tweak the fonts, show date in clock, re-enable the minimize and maximize, allow file manager to handle desktop and draw the desktop and lots more.
The new feature is very simple: you have an on/off switch and when you enable or disable a extension, Tweak Tool will let you know that you need to restart GNOME Shell to apply the changes.
To get GNOME Tweak Tool with Shell extension switching, you must download it via GIT. But don't worry, there's no need to compile it. Firstly install "git-core" (search for it in your Linux distribution repositories), then run the command below to get the latest GNOME Tweak Tool:
cd && git clone git://git.gnome.org/gnome-tweak-tool
Then you should find a new folder called "gnome-tweak-tool" in your home directory. Inside it you'll find a file called "gnome-tweak-tool" - double click it and GNOME Tweak tool should open.
Note: I've tested the latest GNOME Tweak Tool in Fedora 15, but it should work in Ubuntu (using the GNOME 3 PPA), ArchLinux, etc. too. However, it won't work if you've compiled GNOME Shell via jhbuild.
Thanks to ycDref for the tip!