I understand your reluctance to use Calibre. When I first stumbled onto it, I was looking for a simple conversion tool. I didn't want a full library management tool, especially because, as you said, it doesn't allow you to store your files the way you want.
But before you dismiss it, I suggest you ask yourself the following questions:
1. Why do you want to keep your files in your existing hierarchical directory structure?
In my case, I liked dividing my library into a hierarchical system of genres. But as it turns out, custom fields in Calibre give me the same functionality. All my other reasons could be handled with custom fields and the proper save-to-disk template.
In the end, I realized that the main reason I didn't want to use Calibre was because I was too stubborn to learn a new way of doing things. Once I got over my stubbornness, I decided I like Calibre's database system over a hierarchical file system.
And even in cases where I prefer a different viewer than Calibre's internal one, there's always the "Open With" plugin.
2. Is your library so big that having duplicate files is really a problem?
I have over 2000 books in my library, and I'll admit my system is not the most space-efficient. I have at least 5 copies of every book: (1) the original goes into an archive folder, (2) I convert all books to .html and clean them up and store them in a hierarchical library, (3) the .html files get imported into Calibre, (4) Calibre converts them to .epub, and finally (5) I export the .epub to another hierarchical library.
All told, I'm using several gigabytes for my ebooks. But on modern systems, that's not a lot.
3. Even if you don't use Calibre's library management, how much work are you willing to do to convert your library?
As I said before, with proper custom fields and save-to-disk template, you should be able to replicate the file structure you currently have your library in. The drawback is that you have to fill in the custom fields by hand (Update Metadata in bulk is useful in this case). So converting your existing library will probably take some time and effort.
But once you have things set up the way you want in Calibre, converting future books should be fairly simple. Import, fill in the custom fields, convert, save to disk, delete the books from Calibre.
If your library is just sorted by author name, it's even easier because you don't have to set up any custom fields or fill them in. The author's name should be filled in automatically when you import the .mobi file.