Compiling C# to Native?

That's not how ngen.exe works. It merely runs the JIT compiler up front to generate the .ni.exe or .ni.dll module. That binary file does not contain metadata, only the machine code generated from the IL for the method bodies. The CLR still must find the original assembly. Only then can it determine that there is an ngen-ed image available so that it can use the machine code from it rather than generate it from the assembly's IL.

Ngen.exe speeds up the warm startup time of your app, that's all.

My usual advice to anybody that might be interested in disassembling my assemblies is to point them to sourceforge.net. It has terabytes of source code, written and maintained by programmers that are usually better than me. Sometimes even with good comments. If your obfuscator doesn't work well then shop around for a better one. There are many.

I just validated .Net Native on VS2015 & Windows 8.1 (when configured correctly, examine .proj to validate) and building for a particular architecture (may be overkill, haven't validated), will produce a native file which will give you the "harder to reverse engineer" code you are looking for which for me was unabled to read .dll via DotPeek(free .Net decompiler from JetBrains).

Yesterday, at Build 2014, Microsoft announced .NET Native. According to the FAQ, "... Initially, we are focusing on Windows Store apps with .NET Native. In the longer term we will continue to improve native compilation for all .NET applications."