The officer can threaten to do anything he is legally allowed to do. He would have probably been within his rights to detain your son have a drug dog come out and sniff around. If the dog "hit" on the car he could tow the car and apply for a warrant to search the vehicle.
There may be other issues such as: if the officer ran his criminal record then decided to ask to search based on prior offenses, instead of odor or other PC, or if your son invoked his right to counsel or right to remain silent. You need to talk to an attorney about all of the facts to determine if there is anything illegal that occurred.
The medical marijuana card may or may not be of any help negotiating with the prosecutor, or at sentencing with the judge. It does not give him a defense to the charge. The affirmative defense is only available if you have a current prescription and provide the officer with the prescription at the time.
To be convicted of Negligent Driving First Degree a person must be taking illegal drugs. If he had a valid prescription at the time, he had probably had a DUI that was plead down to Neg 1. As such he should already be well aware that he can be charged for DUI if driving under the influence of marijuana, even if he has a medical marijuana card.
I agree with Mr. Lawrence that you should seek legal advice on this. Essentially, the officer was asking for a "consent" search but gained that consent through threats. The "inevitable discovery" doctrine will be in play here. In Washington, the Hammond opinion states that the odor of marijuana from the car is probable cause to arrest the driver for possession. There are many layers of complexity to this issue.
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