I dont understand how defraging will help the download speed... or anything else really for that matter. Care to explain?
During download every transaction in every blocks gets verified against its source transactions. The layout of the data: separate files for index of transactions and actual transaction scripts to causes immense number of disk seeks. Seeking into fragmented files is doubly slow, because the OS has to actualy first seek to the MFT (Windows) or indirect index blocks (Linux).
So the block download process is disk bound not network bound.
I wouldn't actually recommend interrupting the initial download to defragment. Just defragment the Bitcoin directory right before starting the bitcoin{d,-qt} after you haven't run it, say, over the weekend.
This is a kind of pick your poison choice: it is slow on the rotational disks.
If you try to run it off of SSD then bitcoin{d,-qt} exhibits pessimal behavior for the SSD media: very high write amplification of the blkNNNN.dat files and lots of writes with no reads whatsoever in the BerkeleyDB log files (write ahead). If you try to run in on MLC SSD the very act of initial blockchain download puts at least couple of months worth of wear on the MLC flash.
People tried to run bitcoind on the ultra cheap Dell nettops with Linux and 8GB MLC disk drive. Quite often the 8GB SSD would fail before completing the initial blockchain download. This was where Satishi bitcoin was still with WX-widgets, not QT. But the underlying data storage hasn't meaningfully changed. The only otimization thus far was to keep just two most recent Berkeley DB logs instead of the higher, variable number from start to finish.