WCFM has refund settings and refund module.
But this for initiating refund. Refund process totally control by WooCommerce core.
Refund also depends upon order payment gateway.
If any payment gateway support automatic refund then it send refund over api. Payment gateways like PayPal, Stripe etc ..
But some payment gateway does not support this, then Admin has to refund manually.
WCFM has nothing to do here.
Now, you want to refund rhis amount as points. I am not even know which point plugin you are using.
Suppose an user placed order using PayPal but will be refunded as points. This has to be control by that point plugin or tweak using WooCommerce code.
WCFM has nothing to do with this.
If there anything related to WCFM I have already provided you solution!
Please contact your points plugin support for the purpose.
Thank You