There's an old saying I firmly believe in: If it ain't broke, don't fix it.
You could try running defrag in Safe Mode but don't be surprised if it doesn't work.
Defrag in Safe Mode
What is not helpful is that, apparently, with Service Pack 1 of Windows 7, it was decided that Defrag shall not run in Safe Mode. In fact, the DLLs and .inf file associated with it have vanished from all systems where SP1 has been installed. This is another example of the incredibly frustrating tendency of Microsoft lately to quietly remove existing features as part of a new version of upgrade. This may well be the thing that finally alienates the user community enough to switch to the increasingly large number of alternatives.
FWIW, I let Windows 7 do a defrag on an automatic schedule. It seems to keep my machine working just fine. I don't concern myself with what the percentage happens to be at any given moment. Disk Defragmenter Schedule- Turn On or Off