Scope and Sequence for Raspberry Pi Course
I would teach the command line first. Both units 2 and 3 require use of python, which I wouldn't teach before the command line because it is normally run from the command line. I'd also teach the command line earlier because I find that it makes students more comfortable knowing it. It could also be useful because you could teach some command line utilities to connect to the pi and that we prepare the students to learn about networking further.

Generally, teaching shell scripting opens many doors into computer science that I'm sure a few of your students will happily explore. Once you know the command line you can learn how to write command line utilities, explore networking,  process management, and so much more. I think it'd be more effective to get this vital information to students earlier rather than later.