In the book, the assault on the Judgement Day feels more like a clear-cut
situation, with one or few innocent casualties in exchange for vital intelligence and a significant blow to a terrorist organisation bent on extermination of humanity.
The main concern is recovering the data. Several methods were considered but deemed too risky, either because they posed a significant chance of destroying the drives, or because they would leave enough time to the occupants for deleting the data. The filaments were chosen because they were basically immediately lethal to everyone on board (Da Chi even suggested using them during he day to make sure most people would be standing rather than laying in beds), and even if they would cut drives, storage, etc., the cuts were expected to be very clean, allowing for the recovering of most information.
The internal dynamics of the Earth-Trisolaris Organization in the book is also different than in the TV show. The ETO is divided into various factions. The main two are the Adventists, lead by Mike Evans, and the Redemptionists, lead by Ye Wenjie. The former are basically working toward humanity extinction, while the latter are followers of the Trisolaris faith, hoping to save their Lord, either by solving the 3 Body problem, or having the aliens settle on Earth. The two factions are bitter enemies, and are engaged in internal semi-open war, with members of one faction plotting against and killing members of the other.
The JD is crewed almost entirely by Adventists. When planning the assault on the Judgement Day, Wang Miao, the scientist who developed the nano filament in the book, is concerned about possible innocent victims. He's told that an external pilot has to guide the ship during the canal transit, and possibly few of the crew members may be unaware of the ship real nature, but no mention of children, families, etc. It's possible they were onboard and not considered as innocent casualties, but given how the Adventists are portrayed in the book, and the fact they believe some members of the crew to not be part of the ETO, it seems highly unlikely.