When you protest after you resign, you're just a random person without access to the decision-maker's office. Protesting after quitting, away from the office/co-workers would bring about as much attention as me protesting in my home right now.

And let's be serious - they knew they'd be fired. (Or extremely naive)

According to the article, this was effectively a resignation from at least one employee who was quoted as saying he felt wrong to receive a paycheck with money earned from immoral behavior.

You'd have a good point in the case of people working for Bob Everyman, the local grocery store owner.

It's less clear when the "someone" is a nebulous globe spanning transnational with multitudes of projects.

It's moral to work on software that assists humanity while protesting that which does not.

With companies that large your point is akin to claiming it to be immoral to be a citizen of the US while protesting the war in Vietnam.