Fair enough. Maybe you could display an input panel on the view that expects a yes/no value?
import sublime, sublime_plugin
self.window.show_input_panel('Do you really want to overwrite the configuration file (yes/no):', 'No', lambda s: self.handle_response(s), None, None)
def handle_response(self, answer):
if answer.upper() in 'Y', 'YES']:
print 'About to overwrite the configuration file'
print 'Abort configuration file overwrite'