Thank guys,
I have a Wireguard client set up like https://docs.netgate.com/pfsense/en/latest/recipes/wireguard-client.html with a gateway group that prefers routing over Wireguard (tun_wg0) and fails over to normal WAN GW in case of Wireguard failure.
I have found that the best way of disabling Wireguard from GUI is to disable the tun_wg0 interface. In that way traffic fails over to WAN GW.
If I do the same in CLI using ifconfig tun_wg0 down, the interface goes down, but traffic never fails over to WAN GW. What is the CLI equivalence of disabling tun_wg0 in GUI?