We're using VisualSVN Server as SVN server in Windows. But it has very limited abilities for managing rights. Also we couldn't use svn_access_file because our users are going to be authenticated using Windows Authentication method.
Is there any tool to manage rights that uses/supports Windows Authentication?
it has very limited abilities for managing rights
It has all abilities, that Subversion has per se.
we couldn't use svn_access_file
You can and must really, because Windows Authentication define only method of authentication, svn_access_file is authorization file and can refer and use usernames, obtained at authentication stage.