A temporary workaround is to remove the modifier from super and remap the key to a "normal key" you do not use. I choose "µ", which is named "mu".
xmodmap -e 'keysym Super_L = mu mu mu'
xmodmap -e 'clear Mod4'
The first command will pretty much make super useless for anything else than typing "µ" and the second command will clear all Mod4 modifiers (I do not use them anyway). Use xev to find the name of a key, look for a line similar to:
state 0x80, keycode 58 (keysym 0xb5, mu), same_screen YES,
The changes will be lost after logging out. To make them permanent, add the commands to your
.bashrc OR create a file named
.Xmodmap in your home directory with the content:
keysym Super_L = mu mu mu
If you mess up while playing around with xmodmap, just log out and log back in again to restore your old settings.
I've only tested with this one key, and I can still type µ by pressing Alt Gr + M without having Synapse pop up. I also tried remapping Super to Page Up; Synapse was able to detect the key while entering it in the settings, but failed to open the launcher when pressing it.