I have not been able to find any way to have more than one wifi direct group active at this time. However, UstadMobile's Mesharabiya (https://github.com/UstadMobile/Meshrabiya) seems like a possible alternative, if P2P is more important that WiFi direct specifically.

Mesharabiya seems to operate on a combination of WiFi direct and regular access points and appears (at least in recent developer builds) to allow access to the network for all apps, not just a single one.

Note: the intention of this answer is to help people looking for a p2p solution find the right resources more readily. It is not intended as advertisement for Mesharabiya but as a link to a seemingly working implementation with source code available.