Hi!
It is clear from the diagram that the external users query the external DNS server for ftp.domain.com and resolve it to its external (public) IP address.
It is also clear that the server is member of the domain domain.com and is registered as ftp.domain.com with its internal IP address in the AD integrated DNS zone. As this is AD integrated DNS zone it is consistent across the DNS servers and you can not have ftp.domain.com registered with different IP address at the DNS server at Site A and Site B.
A workaround is to register another A name for ftp1.domain.com with the external IP. The users at Site B can use ftp1.domain.com and connect to it using its external IP address.
Another approach would be to use host files for the users at Site B just for the name resolution for ftp.domain.com but I don’t think that is a wise idea.
The main question that stands is what is the benefit from accessing the FTP server at Site A not through the VPN connection. Site B has only one Internet Provider and avoiding the VPN connection for the ftp traffic will not save bandwidth. As for the CPU utilization if you are using serious equipment at Site B like Cisco PIX or Routers, Checkpoint firewall etc. it will not be an issue.
You mention that you have a couple of ISP at Site A so dedicating one of the ISPs to the FTP traffic sounds like a reasonable approach.
Again, I would recommend using a different name like ftp1.domain.com resolved to the external IP of the ftp server at Site B.
I hope this post was helpful.
NetoMeter