would the officer lay charges for running a stop sign on the basis of the dependent witness.
The simple answer is yes. I assume you mean the witness is a friend or family member of the operator of the vehicle that is accused of having run a stop sign. Ultimately it is up to the trier of fact (judge or jury) to determine the weight to be given to any particular witness' testimony but in my experience, interested witnesses can be a persuasive as disinterested witnesses depending on multiple factors. You should discuss this with your attorney.
I assume from your question that there is some dispute in determining liability for a car crash. If you go to trial, the judge or jury (depending on if there is a jury trial) will assess all the evidence presented. That may include the testimony of the two parties, in this case both drivers, and any witnesses. There may be evidence including maps, photographs and information about a traffic device (e.g., information about the timing of lights). The jury will make a determination based on all the evidence. In doing so, the jury will weigh the testimony of each witness in how the person appears on the witness stand, how the testimony comports with other evidence and the interest that a witness may have. An independent witness, one who is not connected to either the plaintiff or the defendant, will tend to have more weight than a family member or friend.
In the end, the jury will judge each witness on both an intellectual level and a gut level: do I trust this person?
As my colleagues have suggested, I would consult your attorney if you are concerned about the impact of a particular witness.