I responded to your post in another thread. But, my fuge is separate from the rest of my system so I simply took it offline. IOW, I turned off the pump supplying water to the fuge.
If you can’t do that, I would just temporarily remove as much of the macro as possible until treatment is done. The Fluconazole MAY kill macroalgae. I will tell you, it did not kill the grape Caulerpa that was in my DT.