This I think is intended to be humorous word play. This portion of the video is "an open letter to disease", and disease is often caused by single celled organisms (microbes). A single-celled organism is "simple" and a multi-celled organism with differentiated tissue types is "complex" in biology.
He's complaining that microbes are "putting themselves at the center of human history" and they don't even care about history. So they are "self-involved" and, like Stan, don't consider the effect that their actions have on other creatures.
Apparently "to imagine complexly" is a phrase used to exhort people to be civil and see other people as complex individuals instead of negatively stereotyping them. This phrase was mentioned in a speech by John Green, who is also this host of the video.
In a speech written for the ALAN Conference, author John Green expanded on the importance of seeing others as complex individuals. Civility issues, misunderstandings, and discomfort on Wikipedia can sometimes arise from a failure to imagine others complexly.
Microbes don't respect the people they are infecting (parasites live in "hosts", so maybe that is another layer of word-play) and Stan didn't respect the "needs" of the show's host, so the host is saying "that's not the way civil people behave Stan!" and at the same time making a reference to simple microbes infecting complex organisms like him. The host isn't serious about this - he's just teasing someone he works with in a good-natured way. Because "imagine complexly" is a concept that the host came up with, he may also be making fun of himself.