It depends what option you want to change...
Some options are tied into commands, like /timestamp, /proxy, etc.
Others can't be accessed. And no, you can't write to mirc.ini and reload it after the program is running.
If the option is commonly modified by users, or if you can convince Khaled why you need to control this option via script, you can add a feature request to create a command to control it from script, but otherwise you will be stuck with Alt+O.
