Hey, whatever works! I suspect the next “major” upgrade for Joomla! is not going to be a “one-clicker” - as version 1.5 (coming soon!) is significantly different in several rather major ways.
There is a lot of talk on the Joomla! forums about that upcoming migration - and it will involve database changes as well as code changes.
The consensus last time I looked was that the “upgrade” process would require considerable “manual” tweaking. All that makes the concern about any “one-click” upgrade possibly moot.
BTW, it is really easy to manually upgrade Joomla! without the help of the CP - almost as easy as it it to originally install it without the CP.
That’s what I have always done, as I can leave the rest of a site functioning (no “empty directory” requirement), which works like a charm as long as you don’t have any files with the same name, or subdirectories with the same name, as the Joomla! install.
It looks like you are probably “good to go”!