I'm no fan of ICE – a very large percentage of my friends in the US are immigrants, and I generally want my country to be a welcoming one. ICE has certainly committed unethical and probably illegal acts (probably true of most federal agencies).
But to expect that a _federal agency_ will be denied service from a private entity, especially for essentially political reasons, is lunacy. It'd attract extreme negative attention from the rest of the government, and great fear from all paying customers that an internet mob could separate them from their code at any time.
We should absolutely be lobbying hard for changes to immigration law, the restrictions placed on ICE, and justice for their wrongdoings.
But I can't see how this helps improve immigration, and it certainly seems likely to cause a lot of negative consequences for GitHub. The employees are putting their employer in a "damned if they do, damned if they don't" situation.
EDIT: Just to clarify, I love the vision of a world where executives don't take actions their workers will protest. I think that in order to get there, the protests need to be reasonable, and I think this one isn't.
EDIT DISCLAIMER: I own a small amount of MSFT stock, which was not on my mind as I wrote this. I use GitHub's free service and have no other relationship I can think of with MSFT or GitHub.
That said, this isn't mere politics. Actual humans can and are dying including children, the individuals at github/microsoft must excercise their conscious and act accordingly. Same applies to war. This isn't akin to refusing service to democracts or republicans but more like refusing service to organized criminals who also happen to be a government agency. All companies have a right and an obligation to refuse cooperation with a government agency that willfully causes death,torture and imprisonment without due process of innocent civilians. That is not a political stance.