Compiler executable file csc.exe cannot be found in .NET 4.5 Azure deployment

I had similar issue. Make sure that you are targeting correct compiler. I was targeting v4.5 (but there shoul be v4.0 as there is now 4.5 compiler)

In web.config check

 <compilation debug="true" defaultLanguage="c#" optimizeCompilations="true" targetFramework="4.0">

Yes, if you have Server 2012, you're definitely running Fx 4.5 and not 4.0, as it's an in place upgrade.

To answer your question in bold, a given ASP.NET app can only use one framework at a time. If you're running as a 4.5 site, then any 2.0/3.5 assemblies should just run as is under framework 4.5.

So my suspicion is that those older assemblies are not the root of your problem.

That being said, I can't explain the csc issue. It might help to include the exact error message that you're getting as well as some of the stack trace.