The best way to solve this on a Site to Site VPN is by using MSS clamping. The actual MSS value depends on the type of VPN used.
Actually these are the simple steps that turn on MSS-clamping for VPN only:
Add this line to $FWDIR/boot/modules/fwkern.conf file and reboot: fw_clamp_vpn_mss=1
Add this line to $FWDIR/boot/modules/simkern.conf file and reboot: sim_clamp_vpn_mss=1
In GuiDBedit on the Network Object of the Cluster:
Set the item fw_clamp_tcp_mss_control to True
On the interface External set item mss_value to 1300 (safe value)
Now reboot the gateway and push policy.
PS to identify the correct MSS value you can use the free tool TCPoptimizer, test through the tunnel and MTU-40 (TCP & IP Headers) gives you the correct MSS value.
Regards, Maarten