I'm mobile on a small-screen phone with a sleeping baby on one arm so please forgive the lack of quoting. Very difficult right now
I believe that demanding anything is only counterproductive. Send in support requests or feature requests, send letters, but do it politely and make it clear that documentation, information, and the ability to do it ourselves is equally as good; if it's truly that important to you and you want to make a statement to Kobo, vote with your wallets and mail them your reader with a polite letter explaining why you won't be buying their hardware. The OpenBSD folks are, IMO, a shining example of how well this works. Linux on the other hand, again in my opinion, tends to have mostly people who not only expect not that they should get what they need to have someone make it work, but rather that companies should do it for them and why isn't it already done!
I'm still not convinced of the utility of having a desktop client, but with sufficient information to do it ourselves I'd be happy to contribute patches to calibre to make it happen. Unless davidfor got to it before I did
Regardless, I think the best first step would be for Kobo to allow setting an account without a network at all, including saying "no thanks, no account for me".
As for this being difficult for non-technical people, how hard would it really be for a developer to write a quick Python script to do it for you? All behind the scene, all the end user does is run the script and say "this drive right over here is my Kobo". If an end user can get online to purchase ebooks, I think it's completely reasonable to expect them to be able to download and run an installer package.
As a technical Linux user, I understand the difficulty in supporting different Linux distros. Debian and Fedora and Ubuntu and Mint and Arch, all different (and yes, Mint is based on Ubuntu or Debian and Ubuntu is based on Debian, but it's not all the same, especially not with Ubuntu's "we have to do it ourselves" mentality) and all requiring ever so slightly (or quite different) instructions. I completely understand their decision to not support Linux. What I didn't mention above, not only do they need to hire Linux developers, they also need to train all their support techs on Linux. Expensive, for dubious business benefit. As much as I (and probably no other Linux user) enjoy, it's the business benefit that will rule. Hence the need for polite information.