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.