IPSec policies are evaluated after post-routing, so you can use src-nat to NAT the two networks against each other and make the IP space unique, and then send the NAT'd traffic via IPSec.
The 'netmap' NAT action can translate whole network ranges easily.
Big question is, what is going across the networks? If there is anything that involves dns resolution from one side to the other, you are gonna have to change the ips on one network.