IO Interactive
Formerly a subsidiary of Nordisk Film (Nordic films) a Danish government run entertainment company.
Later bought by Square Enix.
And recently buying themselves out and becoming an independent company.
>I really wasn't expecting Square Enix to have had a significant role in developing Hitman
They didn't. IO had full creative freedom. All Square Enix did was handle the publishing (and the failed episodic release format)
Atleast according to official sources.