You are in an area where it is worth asking questions like: "Is this really necessary? Might there be some better/easier/more effective way of doing whatever it is that really needs to be done?" And for that, the basic question is "What is it, exactly, that needs to be done?"

Given that the remote unix box has the "required" file and the processing scripts needed for accomplishing some part of your task, what parts of the task need to be done by the windows machine (or the windows user)? To put it differently, what stands in the way of writing a script on the unix machine to do everything, leaving the windows machine entirely out of the process?

If there is data on the windows machine that needs to be folded into the processing, focus on getting that data copied to the unix box, and have a script on the unix box to put everything together.

If some human has to manually inspect data that comes from the unix machine, make some decisions that only a human can do, and then convey those decisions back to the unix machine to finish the process, it would be better to use ssh directly (e.g. via putty), If a GUI is needed, write a perl script using Tk or Wx to create a straight windows app. Doing that sort of job control via CGI would be a last resort, IMHO.