Yes. I have had pretty good success with this method I describe below.
Disable Mac App Store
The App Store is simply not suitable for administration. Barely a quasi-package manager, it is not nearly as useful or reliable as real package managers like pkgsrc, FreeBSD ports, aptitude, RPM, macports or even softwareupdate. In my experience, it is unpredictable and a beard for commercial developers to hock their wares. So there is really only one rational and responsible way, as a competent administrator, to work with App Store:
sudo launchctl unload -w /System/Library/LaunchAgents/com.apple.store_helper.plist
sudo launchctl unload -w /System/Library/LaunchAgents/com.apple.storeagent.plist
sudo mkdir /System/Library/LaunchAgents\ \(disabled\)/
sudo mv /System/Library/LaunchAgents/com.apple.store* /System/Library/LaunchAgents\ \(disabled\)/
And just put it out of your mind, it won't trouble you any longer. ;-)
Use Apple Remote Desktop Admin
Use ARD instead, though not a package manager, it manages packages, installations, updates, and upgrades, it will do what you want, save you time, and will not let you down:
For Apple Remote Desktop 3, for 10.9:
Check out the admin guide first to convince yourself that this is the way to go:
curl -Ok http://images.apple.com/ca/fr/remotedesktop/pdf/ARD3_AdminGuide.pdf
open ARD3_AdminGuide.pdf
Then install:
curl -Ok http://supportdownload.apple.com/download.info.apple.com/Apple_Support_Area/Apple_Software_Updates/Mac_OS_X/downloads/031-2845.20140313.rerft/RemoteDesktopAdmin372.dmg
hdiutil attach -quiet -noverify -nobrowse -noautoopen RemoteDesktopAdmin372.dmg
sudo installer -pkg /Volumes/Apple\ Remote\ Desktop\ 3.7.2\ Admin\ Update/RemoteDesktopAdmin372.pkg -target /
but that might throw a funny error if not running 10.9, or if no previous version of ARD is installed, and if it does, try:
pkgutil --expand /Volumes/Apple\ Remote\ Desktop\ 3.7.2\ Admin\ Update/RemoteDesktopAdmin372.pkg ARDexpanded/
or to equal effect (either/or here, don't need to use both pkgutil and xar... I'm just being thorough):
mkdir ARDexpanded
cd ARDexpanded
xar -xf /Volumes/Apple\ Remote\ Desktop\ 3.7.2\ Admin\ Update/RemoteDesktopAdmin372.pkg
And we no longer need the disk image attached, so eject it:
hdiutil detach -quiet /Volumes/Apple\ Remote\ Desktop\ 3.7.2\ Admin\ Update/
And now what you'll see if you
cd ARDexpanded/RemoteDesktopAdmin372.pkg/
ls
is
Bom PackageInfo Payload Scripts
What's in the Payload file, which is a cpio archive compressed with gzip, is what you're after. So with a few piped commands we can get to the app bundle:
cat Payload | gzip -d - | cpio -id
ls
returns:
Applications Bom Library PackageInfo Payload Scripts
And you're nearly done.
cp -R Applications/Remote\ Desktop.app /Applications/
Now you have installed Apple Remote Desktop Admin 3.7.2
So all that's left to do is purchase your license:
open http://store.apple.com/us_smb_78313/product/D6020Z/A/apple-remote-desktop-3-volume-licenses-20-seats-price-is-per-seat
Launch /Applications/Remote\ Desktop.app and serialize. And get some work done.
For 10.6 Snow Leopard, you'll need a slightly earlier version of ARD:
curl -Ok http://images.apple.com/ca/fr/remotedesktop/pdf/ARD3_AdminGuide.pdf
curl -Ok http://supportdownload.apple.com/download.info.apple.com/Apple_Support_Area/Apple_Software_Updates/Mac_OS_X/downloads/041-6789.20120917.xD6TR/RemoteDesktopAdmin353.dmg
hdiutil attach -quiet -noverify -nobrowse -noautoopen RemoteDesktopAdmin353.dmg
sudo installer -pkg /Volumes/Apple\ Remote\ Desktop\ 3.5.3\ Admin\ Update/RemoteDesktopAdmin353.pkg -target /
and if it throws back at you this:
installer: Cannot install on volume / because it is disabled.
installer: This update could not find Remote Desktop on this volume.
then try:
pkgutil --expand /Volumes/Apple\ Remote\ Desktop\ 3.5.3\ Admin\ Update/RemoteDesktopAdmin353.pkg ARD353
hdiutil detach -quiet /Volumes/Apple\ Remote\ Desktop\ 3.5.3\ Admin\ Update
drill down to the Payload:
cd ARD353/RemoteDesktopAdmin353.pkg/
ls
returns:
Bom PackageInfo Payload Scripts
So run:
cat Payload | gzip -d - | cpio -id
ls
returns:
Applications Bom Library PackageInfo Payload Scripts
And you're nearly done:
cp -R Applications/Remote\ Desktop.app /Applications/
purchase your license:
open http://store.apple.com/us_smb_78313/product/D6020Z/A/apple-remote-desktop-3-volume-licenses-20-seats-price-is-per-seat
Launch /Applications/Remote\ Desktop.app and serialize. And get something done.
Remove users' admin rights
Also, you may want to deeply consider removing admin rights for your users; although this will create more work for you if your users often need to authenticate with admin passwords, it may also help prevent "bad things." And if you have ARD installed, you can connect to their logins from your desk to authenticate for them remotely.
Best Answer
I'm not sure what's going on with the App Store update, but I have a guess about the downloaded update: did you get the "OS X El Capitan 10.11.6 Update" (759.1 MB), or the OS X El Capitan 10.11.6 Combo Update (1.5GB)? If you downloaded the first one, it won't work because it's only capable of updating from 10.11.5 to 10.11.6; since you have 10.11.2, you need the "combo" version, which rolls in all of the earlier 10.11.x updates, and is therefore capable of updating from any earlier version of 10.11 to 10.11.6.
(BTW, this requirement is listed on the download pages for the two updates, but you have to click "System Requirements" to actually see it, and even then it's not very explicit. The first says it requires "OS X El Capitan 10.11.5", but the second just says "OS X El Capitan 10.11".)