It's a collective action problem - the company can't fire the first engineer if they know everyone else they hire would also refuse orders. But each individual engineer has an incentive (not getting fired) to break with the group's strategy.

This collective action problem is solved by coordination, through the means of the licensing body. That body can impose severe penalties (not just firing you from your current job, but from all future jobs) for anyone who betrays the group strategy, so an individual engineer can feel some more safety refusing orders in the knowledge that the whole profession will back them up.

EDIT: In civil engineering, this system is propped up by the state, which requires plans to be signed off by a licensed engineer. The guild functions in this capacity as a subcontractor of the state, taking on a regulatory burden and allowing rather more severe punishments (barring someone from a profession) than would be acceptable from a purely state organ. In software, this could be enforced by similar means for safety-critical applications - the ACM, for example, could be required to license any software engineer, with the understanding that they would revoke licenses for negligence or malfeasance that didn't rise to the level or criminal liability.

While skilled software engineers are still rare enough to be coveted, programmers are a dime a dozen these days, many desperate to get their foot in the door to break into the industry. Licensed engineers, on the other hand, are hard to come by. Professional engineers spend years in school, then years training under a licensed engineer, and then finally take an arduous test with an abysmal passing rate to get their license. They aren't about to risk their entire career to satisfy some asshole manager, because the entire business depends on the engineer, not the other way around. It's a small community and word gets around.