Well, I can think of two ways.
The first and simpler way would be to ignore the timer altogether and just have a parallel process do the job for you. You have it set so that it adds 1 to a variable "Weather" or such, and then guage what the weather should be based on that variable (make sure to reset the variable at some point).
The second way would be to go in and edit the scripts a little bit, so that you can make it visible or invisible by turning on a switch.