Should I wear my aligners with gum recession?

Was there recession before you started Invisalign? Sometimes, when your teeth are very misaligned, you may not have noticed. 
Invisalign should not cause recession - they are designed to be slow-moving. Depending on how much recession you have, I believe you need to know what it causing recession. For instance, clenching or grinding teeth can cause abfractions, which can cause recession, and, yes, aligners function like an occlusal guard, but an occlusal guard won't stop a person from continuing to destructively grind and clench. I routinely evaluate and use Botox therapeutically to help control excess muscle activity. 
I don't believe that you should have a gum graft until movement with Invisalign is completed and stabilized. If you wish to stop Invisalign treatment and graft first, you may see recession occur again when treatment starts again.