You can go to Apple.com and download any Apple Updates manually: http://support.apple.com/downloads/

And there's no harm in "reapplying" them. In fact, sometimes it's a good troubleshooting measure.

Yes. I have had pretty good success with this method I describe below.

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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. ;-)

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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.

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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.

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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.