Nah, it wasn't bad at all. The whale extinction plot was to raise awareness of the discovery of whale intelligence and to spark resistance against the immorality of whale hunting. Perhaps it was a little hamfisted, but Star Trek was always woke as hell.
Star Trek has never shied away from telepathy, so it wasn't much of a stretch to have the whales in contact with a powerful alien intelligence elsewhere in the galaxy. It wasn't the lack of whales that caused ships to shut down and Earth's weather to whip up hurricanes, but rather the overwhelming energy field of the probe the aliens sent to investigate the silence.
All that and it somehow managed to showcase an absolute banger punk song raging against nuclear holocaust.
