So, essentially, the pamac GUI should refuse to run when… there’s a GUI running? 
You know what? Just be smart, log out of your GUI, log in at a tty and run the update with pacman. Success guaranteed, and it’s what I advise for every bundled update.
For individual packages or small package groups — say up to 5 packages — you can use the pamac GUI, as well as for installing or removing small amounts of packages. But do yourself a favor and run bundled updates from a tty by way of pacman. Far less trouble! 
Note: There’s also octopi, which uses pacman and an AUR helper in the background. The only downside — if applicable — is that it doesn’t handle Snaps or FlatPaks.
