No. run is defined as executing a script, and scripts always have access to the current workspace and affect the current workspace (though in some very recent MATLAB versions there are starting to be some ways in which scripts do not have full access to private information.)
You could create a wrapper function that looked in its parent function and copied all of the parent's variables into the current workspace, and then ran the script, and then looked at all remaining variables and compared them to the parent's copies of the variables in order to determine which had changed, and then write the changed versions to the base workspace. This would be somewhat troublesome, but I guess there might be some use for it.
If you did not want the script to have access to any of the current workspace's variables while it ran, then you could
evalin('base', 'run(''script.m'')')
