The simple answer is no. The long answer is...
NTFS does store filenames in a case-sensitive way (NTFS can have README.txt and readme.txt in the same directory), and even the Windows filemanager can internally manage case-sensitive requests to filenames via the NtOpenFile / NtCreateFile syscalls.
Unfortunately for you, the Win32 function CreateFile (used everywhere including by fopen) will internally call NtCreateFile using the OBJ_CASE_INSENSITIVE flag which will mean that all applications which use CreateFile will see your case-sensitive filesystem case-insensitively. In practise this means that all applications will see your filesystem in a case-insensitive way regardless of whether your filesystem is actually case-sensitive under the hood.
The only way I can think for you to practically force case-sensitivity is to write a filter-driver which will remove the OBJ_CASE_INSENSITIVE flag from the incoming syscall requests which will then allow NTFS, EXT2 or whatever internal filesystem you have to behave in their default, case-sensitive way.
This is a fallback from DOS where filenames were not case-sensitive, and MS-Windows is built to be compatible with this user-friendly feature. Unfortunately, if NTFS was suddenly switched to being case-sensitive, then a lot of things would fail (and the OS probably wouldn't boot at all) as you'll be able to find case-insensitive variations throughout the Windows Registry (e.g., C:/WINDOWS/, C:/Windows, C:/windows, etc.) and in various configuration files (and probably some hard-coded stuff too). Windows and many applications would need some major work to support this for drive C: at least. – Randolf Richardson – 2011-09-09T17:36:12.060
Look at this post I think it might help you out.
http://superuser.com/questions/266110/how-do-you-make-windows-7-fully-case-sensitive-with-respect-to-the-filesystem
That's what I was asking actually: How to avoid turning NTFS file handling globally case-sensitive on Windows :) So I would need some sandboxy tools, an installable file system or something like that. Like those ext2 drivers up there. The only requirement is they must respect the letter case when identifying files. – Ivarpoiss – 2011-09-09T19:28:38.460