As far as I know, most IPSec VPN solutions allow to enable split
tunneling. The client's non corporate traffic does not get routed
via the corporate VPN. (Some companies may turn this OFF because they
don't want a client access the corporate network while possibly being
remotely monitored or controlled by an internet attacker.)
Do you know what VPN solution you are using. This is something for the
VPN/Firewall/Router sysadmin to manage.
Are you using Samba 3 or Samba 4- you could probably get traffic
running over ports 137, 138 and 139 since Samba 3 doesn't actually run
file traffic over 445.
However, I don't think the Windows file server protocol (samba or not)
was really designed for heavy use over the internet. Even "fast"
internet links are slow compared to most LAN speeds. It might be ok for
people copying files back and forth but not editing files directly from
network shares. (from my experience.) You may be better off
looking at a remote desktop type solution for a some of the users .
It also seems incredibly insecure to have a file server directly
accessible from the Internet.