The militia system is not super well integrated into the campaign, IMO. Most of the actions don't really do anything unless you do a lot of additional work-- making enemy bases teams can attack and stuff. Cool stuff could probably be done with the militia system, but I don't think Ironfang really has that groundwork.
As such, I'd recommend thinking about ways you can make the spirit of the different actions seem relevant. So sure, have your teams making shelters or crafting.
Honestly, I probably wouldn't bother with militia rules until you get the refugees into the Cradle of Stone. Up until then the group should be too busy trying to survive to form a militia.the survival rules are going to be your friend instead. You can assign NPCs to hunt or make shelters with those. (I don't think there are rules for them crafting but at least one named NPC from the book can make items for you.)