Powershell to the rescue:
function SetSafeAgainstScriptTrue($url) {$webapp= Get-SPWebApplication $url$path=$webapp.IisSettings.get_Item(0).Path.FullName +"\web.config"$now=[datetime]::now.ToString('yyyy-MM-dd') Copy-Item $path"$path.$now" Write-Host "Backupped" Write-Host "Modifying web.config file in path $path" (Get-Content $path) | Foreach-Object {$_-replace"SafeAgainstScript=`"False`"", "SafeAgainstScript=`"True`""} | Set-Content $path }