The squirrel example sounds terrible, but people don't realize the danger that moving pathogen-carrying specimen across ecosystems poses. Introducing a disease into your local environment can have devastating consquences for wildlife or farming or both.

Example: Dairy farms have strict rules about not letting anybody in who was abroad within the last 48 hours because of possible spread of foot-and-mouth disease. There are many such examples and similar examples exist for wild ecosystems.

So, while it may seem cruel to kill a few hundred squirrels, the precaution is justified. The "guilt", if there is any, is with whoever didn't ensure all the paperwork is in order.