Unfortunately the Defragmentation tool cannot be run in Safe Mode as the service won't run in Safe Mode. It is by design.
Defragmentation used to run in safe mode for earlier version of Windows but not in Windows 7
You would receive the following message if you try to run Disk defragmenter in Safe mode on Windows 7.
“Windows could not start the Disk Defragmenter service on Local Computer.
Error 1084: This service cannot be started in Safe Mode”.
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