Exactly! We should absolutely have groups of people inflict violence on anyone who opposes my political beliefs! (Don't worry, my political beliefs are the true and virtuous ones, other political beliefs are evil and corrupt)
...which increases the cost of doing business for those companies.
And if eco-terrorists are successfully killing their directors, then they are probably also setting fire to their offices, mailing poison to managers, sending death threats and hate mail to employees, vandalising company property, calling in bomb threats to their refineries, executing those threats...
The benefits outweigh the costs. Openly employing private armies with full government support, randomly arresting suspected eco-terrorists and their families, holding them indefinitely at undisclosed locations, raiding or UAV bombing reported gathering locations etc.