"deprecate" and "remove" are not synonymous and I don't see any indication they are being conflated here. Deprecation often precedes removal but that's the extent of it.
Deprecation generally means continued use of tool/API/etc. is actively discouraged. Users of a deprecated tool/API/etc. should find a suitable alternative for all their remaining use cases. In this case, once this shortener is officially deprecated, anyone using a git.io URL for any purpose should replace it with an alternative.
Deprecation is usually a precursor to removal. Once the tool/API/etc. has been deprecated long enough (relatively speaking), it's generally consider as safe as practical to remove the tool/API/etc. from service. That lead time can range anywhere from months to years.