Your prior seems to be that the Trump administration is operating in good faith and that they would naturally be predisposed to allow the merger, being free market republicans and all.

That's not the accusation at hand. The contention is that the Trump administration is threatening to block the merger (corruptly, in opposition to their republican proclivities) unless the news arm of the merged company is operated in a partisan way.

And the evidence for that is that Ellison walked in, threw out CBS News's pre-existing leadership, and brought in a reasonably-well-known-but-still-not-celebrity-enough-to-be-independent partisan republican voice to run it. And now that she's there, she's clearly operating the news room in a partisan way.

Seems like a pretty convincing theory to me.