You can put AllowOverride directives inside <Directory> containers in httpd.conf, with the <Directory> containers specifying directories which can and/or cannot use .htaccess. Example:
Code:
# Default to allow all to use .htaccess
<Directory /*>
AllowOverride All
</Directory>
#
# Disable .htaccess in this path
<Directory /cannot/use/htaccess/*>
AllowOverride None
</Directory>
#
# But turn some features back on for this one dir in the above path
<Directory /cannot/use/htaccess/but-this-one-can/*>
AllowOverride FileInfo Options
</Directory>
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