It would be a VERY good idea to add an option for case-insensitivity in file ordering in thunar. If, for sake of semplicity, you don't want to add it, I'd definitely prefer thunar to be case-insensitive (currently it's case-sensitive), as it's way more natural for humans. just my two cents.
The default has been set to case-insensitive several months ago. See bug #2064. *** This bug has been marked as a duplicate of bug 2064 ***