I delete the old backup when I have verified the integrity of the new one ( Acronis True Image 9 ). This causes a lot of fragmentation so I defrag my External USB drive on which the backup is stored once a month. Not sure why it should be any different to defragging ones main C Drive as and when necessary.
If you are really worried about defragging corrupting a hd with your backup on (and I don't think it will) copy the backup archive across to your main HD temporarily and then copy it back after defragging, it will not be fragmented when you copy it back.
I have been given the advice from a PC technician that the best compromise after reading these comments would be to "defrag" ones own PC before a complete backup to external hard drive. This means the backed up information will be defragged before transfer.