I am trying to setup a window breaking using the Cell Fracture and Rigid Body features. However, the mesh clearly shows the tiny fracture lines before the collision so the illusion is immediately broken. This is made all the more obvious when I use a glass texture as the transparency shows all the lines.
How can I disguise the initial cracks? Or do I need to edit a clean pane with the fractured pane?
What you need to do is to disable the visibility and renderability of the glass shards until the impact. And, before that, you need a non-broken pane to take their place.
The easiest solution for that (altho still tortuous) is to set the non-broken pane alone on a layer and all the shards together on another layer. Then you animate the inclusion of the layers in the scene depending on your needs. (See the Layers panel on the Render tab.)
The other way is to animate the visibility and renderability directly in the Outliner. That can be a very tedious task if you have a large number of shards.