The head of the S.D.N.Y. office is Geoffrey Berman, a Trump appointee. Berman has recused himself where that is appropriate and pushed ahead where that is appropriate. The people on his team are famously independent professionals.
While on my second reading of James Comey's A Higher Loyalty, I think if there's any political sphere in America from which we can garner some hope, it's the institutions of our public and private justice systems. While general public and media can pass off justice (by extension of the disorder of law enforcement) as an enabler of political thuggery, these guys have been as rebellious and insurgent when necessary to defend American values than anyone as far as I'm concerned.