Latvus, in the aforementioned article, interestingly notes the parallel between Gedaliah’s instructions to the people to submit to and not fear Babylon, so that “it shall be well with you” and the Deuteronomic exhortation to obey Yahweh so that it will be well (Deuteronomy 4:40; 5:16, 26; 6:3, 18; 12:25, 28; 22:7).  The point is “Contrary to the main line of deuteronomistic history, in this passage it is the foreign nation, not Yahweh, which should be served.”  This is evidence of the writer’s “subordinated attitude” toward empire.

Well, no.  Yahweh has given dominion to Nebuchadnezzar.  Therefore submission to him is submission to Yahweh.  That’s the logic of Jeremiah 29, which Gedaliah quite correctly repeats.