Note that MSFT isn't denying the use of Microsoft Office or Outlook to the FBI et al. That's essentially what GitHub's employees are asking for. They're denying the use of a tool which can be directly used to do harm, until they're sure it'll be used appropriately.
If a tech company were supplying software that was a key enabler for ICE's cruelty (such that ICE's cruelty would be significantly hampered without the tool), by all means they should stop the sale.