Jesse Noakes, 34, Emil Davey, 21 and Matilda Lane-Rose, 19, pleaded not guilty in Perth Magistrates Court on Tuesday to conspiracy to commit criminal damage.
Counter-terrorism police were waiting for the Disrupt Burrup Hub trio when they arrived at chief executive Meg O'Neill's home on August 1 with an ABC camera crew while she, her partner and their daughter were inside.
The group was taken into custody and charged amid allegations they illegally trespassed onto Ms O'Neill's property with yellow paint, water balloons and a bicycle lock to intimidate her.
A police prosecutor detailed facts of the incident for the court, which included the activists allegedly visiting a park across the road from Ms O'Neill's home and a Bunnings store in the days before the protest.
The prosecutor also applied to have the matter elevated to the District Court, which is usually reserved for more serious matters and where the punishment could have been more severe if the group was convicted.
But he was forced to withdraw it after Magistrate Thomas Hall pressed him to justify the application.
"I would have thought so as well unless the offending was horrific," Mr Hall said in response.
Disrupt Burrup Hub's lawyer Zarah Burgess also agreed with the decision to cancel the application, saying: "Some sensibility at last".
Outside court, Ms Burgess spoke more about the failed protest action which Premier Roger Cook previously said was carried out by "extremists" attempting to "terrorise".
She said Lane-Rose was "ambushed" by more than a dozen counter-terror police who were "lying in wait" inside Ms O'Neill's home and Davey was arrested at gunpoint by police before the incident.
"Jesse Noakes was sitting in a parked car with the engine still running and never left the vehicle until ordered to do so by police," she said.
Ms O'Neill on Friday said she remains concerned about the threat posed by the activists, and that the incident was "extremely distressing" and she worries for her family's safety.
She is understood to be scheduled to appear in a Perth court on Friday after taking out violence restraining orders against some Disrupt Burrup Hub members following the incident.
The Burrup Peninsula, in WA's Pilbara region and known as Murujuga to traditional owners, contains the world's largest and oldest collection of petroglyphs.
Disrupt Burrup Hub claims Woodside's operations in the area and its proposed expansion form the biggest new fossil fuel project in the country and could produce billions of tonnes of carbon dioxide by 2070.
It has carried out a series of actions against Woodside this year including the release of stench gas at the company's Perth headquarters in June, forcing the evacuation of about 2000 staff.
Noakes, Davey and Lane-Rose are scheduled to return to court on January 30.
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