Unless there is at least one photo showing a red light and your car before it enters the intersection, the fine should not stand. In fact, the light should be "steady red" according to the vehicle code, which courts have interpreted as meaning at its full brightness, which can take .1 to .4 seconds, depending on what kind of light it is.

You should also be able to view the online video, which should confirm what the photos indicate. If what you're saying is correct, you might be able to get the whole matter disposed of by just calling the police agency involved. If you're dealing with the court clerk on this, you won't get anywhere. If you've received a Notice to Appear in court, you should complete a Trial By Written Declaration which you can learn about online or on your citation copy.