As far as I know:
an user with not enough permissions may not be able to create/write the config file
You should be able to make files inside user's "home directory" or "application data" directory, regardless of permissions. Normally those directories should be writeable.
would todays antivirus allow me to add/edit/remove keys?
Haven't ever seen my antivirus interfere with registry manipulation. You probably will be fine as long as you aren't doing anything suspicious in registry.
Which way would be better?
It is matter of taste. I think that text file is better - allows easier migration of settings. Just don't leave junk behind after uninstall.
Also, if someone knows a class/lib to manage config settings in vc++
QSettings in Qt 4. But using entire Qt for just saving settings is definitely an overkill. You could also check configuration languages like JSON, use lua for settings (less overkill than using Qt 4) or get any XML library. Also, working with registry directly or writing configuration files using iostreams or stdio shouldn't be hard. And you can always write your own configuration library - if you feel like it.