To be honest I do not really understand, you get an option to select what target you want to use, and whatever you choose it uploads to, choose local and your remote files are untouched.
Sorry but maybe I am missing something, because I do not work locally, and am not really seeing the problem.
Maybe a pop up should appear when you are selected on your remote target, and on save the pop up says, Warning, you are selected on your remote target. With a checkbox that says never show this warning again, that way for people developing on remote targets they can just choose to never see it, and for people developing on local targets they can keep the warning up, so if they forget to change their target they are reminded each time before the save happens.
Surely that will cover every eventuality.