At this point, the only known and working solutions on this issue are the following:
There are currently two Group Policy options to control the Store tile pin - one that you can use before deploying the update that will prevent the Store app from being pinned to the Taskbar, and another that you can use after the update has been deployed and the Store app has been pinned to the Taskbar.
Option 1: Turn off the Store application before Installing the Windows 8.1
Use the Group Policy “Turn off the Store application”
As mentioned earlier, the Store Icon is pinned to the Taskbar at first logon after Windows 8.1 Update is applied. The Store application will not be pinned to the taskbar if the GroupPolicy “Turn off the Store application” is applied to computer. This option is not retroactive. The Group Policy must be applied to the workstation before the update is applied. The full path to this Group Policy is:
Computer Configuration\Administrative Templates\Windows Components\Store\Turn off the Store application
User Configuration\Administrative Templates\Windows Components\Store\Turn off the Store application
You can use either Group Policy. As the name of the policy indicates, this will completely disable the Store.
If your desire is to allow access to the Store but do not want the Store tile pinned to the Taskbar see option 2.
Important note: By default the Group Policy setting “Turn off the Store application” will not show up in GPEDIT.MSC or GPMC.MSC if you run the tools on a Windows Server. You have two options: Install the Remote Server Admin Tools (RSAT) tools on a Windows 8.1 client and edit the group policy from that machine or install the Desktop Experience feature on the server used for editing Group Policy. The preferred method is to install the RSAT tools on a workstation. You can download the RSAT tools for Windows 8.1 here: http://www.microsoft.com/en-us/download/details.aspx?id=39296
Option 2: Use Group Policy to remove Pinned applications from the Taskbar after Installing the Update
Use the Group Policy “Remove pinned programs from the Taskbar”
This GP is a big hammer in that it will remove all pined tiles from the task bar and users subject to the policy will not be able to pin any applications or tiles to the Taskbar. Thisaccomplishes the goal of not pinning the Store tile to the taskbar and leaves the Store accessible from Start.
User Configuration\Administrative Templates\Start Menu and Taskbar\Removed pinned programs from the Taskbar”
The last available option at this time is to have users unpin the Store app on their systems. Programmatically changing the Taskbar pins is not supported nor encouraged by Microsoft. See http://msdn.microsoft.com/en-us/library/dd378460(VS.85).aspx
If you'd rather not have Modern Apps taking up that precious real estate on your Taskbar, once again, we provide you the choice of configuration.
As a note on the above:
The Store app is pinned the first time the user logs into a machine after installing the 8.1 Update is installed or for any new user profile created on the machine after the update was installed. So the GP would need to be active before either of the two. Also, if the user’s profile already has the Store App Pinned and the GP is applied later, this won’t unpin the Store App
Additionally to this:
You cannot perform either any operation on this area programmatically – since you will be in an unsupported state (as stated below).
“A small set of applications are pinned by default for new installations. Other than these, only the user can pin further applications; programmatic pinning by an application is not permitted.”
There might be another fix on this issue on a future update of Windows, but right now we are not aware of any definite decisions or timeframe on this.