The LONG version is that you'll have to use DOM functions to find the client ID of the control you want to update, then just set it's value.
I can probably find some sample code for you once I get to work if no one else beats me to it...
EDIT:
Basically all you need to do is:
HTMLDocumentClass doc = webBrowserControl.Document as mshtml.HTMLDocumentClass;
HTMLInputElement input = doc.all.item("checkboxID", 0) as HTMLInputElement;
input.value ="false"; //Could be 0, not sure...
//could also be input.@checked = false, sorry I haven't actually used this on a checkbox before... one of these should work though
So yeah, not sure why anyone would go through all the effort to write a JavaScript and invoke it when you can set a control's value with 3 lines of code.