I apologise for not tackling this on my own first i have no idea is it possible to change the opacity relevant to how much light is hitting the object?
I think you could do this one of two ways. Approach 1 would require a custom shader. Approach 2 would require you to get the distance from your object to any lights shining on it, and change the opacity manually based on how close/far it is. This is pretty similar to how much light is shining on the object, but not identical.
In approach 2, the opacity affects the whole object (thats more or less what im doing now) I just want to affect the faces that are being shone on
I bet the Shader that Aras was kind enough to write for me dealing with Saturation could also be tweaked to affect Transparency based upon lighting. http://forum.unity3d.com/viewtopic.php?t=4538