The update files wizard has several steps to filter out files you do not want to update. e.g. their workflow state, their directory, their filename, their configurations, only files that are checked out.
However yeah, if they go through all of those filtering steps and still have chosen to overwrite a value, I cannot think of a way to stop them.
I think most typically people would control this with the workflow state filter....i.e. don't update files that are in the released state...and if the users don't have checkout rights to the released state, they couldn't overwrite those if the wanted to.