ASP.NET MVC - Visual Studio Publish Not Override Destination Web.Config - asp.net

Question

I am new with ASP.NET MVC and just started playing around with it. I am building a test project on my desktop and publish it on the Development Server (IIS). After I published on IIS server and I received this error below:
Compiler Error Message: CS0433: The type 'System.Web.Mvc.WebViewPage<TModel>' exists in both 'c:\Windows\Microsoft.NET\Framework\v4.0.30319\Temporary ASP.NET Files\test2_aspx_datatableeditable\8a6a3e30\832ace90\assembly\dl3\264e4d37\00038593_07d9cf01\System.Web.Mvc.DLL' and 'c:\Windows\Microsoft.NET\assembly\GAC_MSIL\System.Web.Mvc\v4.0_3.0.0.0__31bf3856ad364e35\System.Web.Mvc.dll'
I then read different posts related to that error above and some suggested to remove the this statement below in the Web.Config file. After I removed the code below, it worked fine.
<add assembly="System.Web.Mvc, Version=3.0.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35" />
Now, the problem is that every time I made some updates and publish from VS-2014, it overrides the web.config file, and then I have to remove the line of code in the web.config again in order for it to work. I also tried to Right-Click the web.config file and set Build Action to None, but it didn't seem to work either.
I really don't want to go to the Output folder and keep remove the code line above in the web.config every time I publish it. Is that anyway to NOT override the destination web.config only?
Thanks in advance,
Below is my simple web.config. Please help with a sample code if web.config transform is a best option.
<?xml version="1.0"?>
<!--
For more information on how to configure your ASP.NET application, please visit
http://go.microsoft.com/fwlink/?LinkId=152368
-->
<configuration>
<appSettings>
<add key="ClientValidationEnabled" value="true"/>
<add key="UnobtrusiveJavaScriptEnabled" value="true"/>
</appSettings>
<system.web>
<compilation targetFramework="4.0">
<assemblies>
<add assembly="System.Web.Abstractions, Version=4.0.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35" />
<add assembly="System.Web.Helpers, Version=1.0.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35" />
<add assembly="System.Web.Routing, Version=4.0.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35" />
<!--<add assembly="System.Web.Mvc, Version=3.0.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35" />-->
<add assembly="System.Web.WebPages, Version=1.0.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35" />
</assemblies>
</compilation>
<authentication mode="Forms">
<forms loginUrl="~/Account/LogOn" timeout="2880" />
</authentication>
<pages>
<namespaces>
<add namespace="System.Web.Helpers" />
<add namespace="System.Web.Mvc" />
<add namespace="System.Web.Mvc.Ajax" />
<add namespace="System.Web.Mvc.Html" />
<add namespace="System.Web.Routing" />
<add namespace="System.Web.WebPages"/>
</namespaces>
</pages>
</system.web>
<system.webServer>
<validation validateIntegratedModeConfiguration="false"/>
<modules runAllManagedModulesForAllRequests="true"/>
</system.webServer>
<runtime>
<assemblyBinding xmlns="urn:schemas-microsoft-com:asm.v1">
<dependentAssembly>
<assemblyIdentity name="System.Web.Mvc" publicKeyToken="31bf3856ad364e35" />
<bindingRedirect oldVersion="1.0.0.0-2.0.0.0" newVersion="3.0.0.0" />
</dependentAssembly>
</assemblyBinding>
</runtime>
</configuration>