Yeah, arguably another merchant may not be as big a "must fix" as the other things.
It's not so much the time between the Harbour and entering Cyseal that I'm concerned about in terms of weapons, it's what happens if you beat the Sparkmaster, but one of your guys's weapons is lagging behind, and you have been unlucky with drops. I can assure you that when I ran a rogue, he required revisiting the existing shops a few times because with an out-of-date weapon, his damage output plummeted badly.
Beating the Sparkmaster is the trigger for Anna to leave, so if you can't, then she'll still be around.
The hypothetical quartermaster could have a high repair skill as well.