Replicating development environment with Android

I agree with Richard, you should be able to set breakpoints and step through code using Eclipse with the Android Development Tools plugin.
However on the specific question of building a Visual Studio app without the inclusion of any Windows specific definitions. It can be done but it's not all that easy. I've been into this because I'm developing a cross platform framework which necessitates being able to take the same source and build an exe for many platforms without modification.
The key Visual Studio C/C++ Properties to look for are 'Ignore Standard Include Paths' under Preprocessor and 'Ignore All Default Libraries' under Linker/Input.
With these settings you can stop VC pulling in anything Windowsy automatically. Then you'll need to manually add in everything you do need.
One thing to remember is that no matter how standalone an exe is it must link to Kernel32.lib to be a valid Windows executable. There are rumours of a new security check added under Vista to enforce this although I haven't tried it out. In practice it's almost impossible to write a useful exe that doesn't link Kernel32 anyway.
If you can point the C/C++\General\Additional Include Directories at the location of the Bionic C library headers then there's some chance of being able to use C library functions but you'll need an x86 build of Bionic to link with. This may be available from the Androidx86 project depending on version compatability.
I wish you luck. It rather sounds as though you might need it.