I think this is a particularly distinctive case, for example, by comparison to the recent news that Amazon is blocking law enforcement access to Rekognition (facial recognition). Facial recognition and AI in general is fraught with massive ethical concerns to the point where leading developers/researchers in the field are actively abandoning it (e.g. YOLO). There's no such concern about development of source control, certainly no more so than would apply to any business productivity software, or virtually any networking, infrastructure, or database projects. Interestingly, this may signal a developing rift between Open Source licensing ethos which strictly forbids limitation on use, running head-on with political agendas which would seek to limit access to software based on the user. Licensing isn't really a concern in Github's case, but will be a consideration that developers have to make when choosing a license in the future, namely... do I release my software as Open Source and give up my right to stop Bad People from using it for their own benefit?
For a company like GitHub (owned by Microsoft lest we forget) to cut off access to a branch of the Federal government would be extremely foolish, but I believe also not only counter-productive, but also ethically questionable and politically dangerous. I don't believe Github (or most any workplace) should be a political battleground for debates over border policy, and I believe that a vocal minority attempting to weaponizing neutral parties like Github leads to bad business outcomes (lost income, hostile workplaces) as well as bad political outcomes (breeding resentment and polarization).
As far as the particular issue of cutting off ICE from its source control software, I think a less political assessment would find that it's in the best interest of immigrants and refugees for ICE to have top-notch software custom built for the populations that they oversee. I'm not particularly familiar with the many tasks that ICE officers perform on a daily basis, but I know that things like trying to process hundreds of thousands of refugees applying for asylum, or trying to place ~50,000 unaccompanied minors in homes throughout the country is a truly massive logistical challenge, and we don't want a single child slipping through the cracks. Cutting off ICE access to software development tools IMO is actively harming these populations.