Actually, already in CBSubs 1.0.3 which is released, there is an undocumented feature that you could use for this, provided you don't need to mix in the same purchase the 2 payment methods !
In plans and in gateway accounts you have a field present, called "owner" defaulting to 0.
When a user purchases a product (subscription, donation, or merchandise), CBSubs will offer as payment methods only gateways which have same "owner".
For a good chance of forward compatibility, you should use owner 0-3 for now. E.g. giving owner 0 to one plan and gateway account and owner 1 to the other plan and gateway account.
That should work fine for your case
Let us know how it works out for you
Note: this is an undocumented feature which will be evolving in future releases, so we can't grant backwards compatibility, but the current basic multi-account feature will be integrated into more advanced ones.