Is there any plugins which can disallow some of the users/domains to login to roundcube even they have IMAP/POP login
No, nothing that I know.
But you could have a look into my DNSBL plugin (see links in signature) and modify it to block specific users.
if you know the accounts which you want to allow login then you could log them in once and then set auto_create_user to false so no other accounts will be allowed. That depends if you know the ones you want to allow or only the ones you want to block.