What webmin does is direct edit the configuration file. E-Smith will recreate the configuration file from the templates. This makes any Webmin changes temporary.
The unless webmin gets edited to alter template fragments and expand-template then the two wil *always* be incompatible.
As for MySQL - there's a contrib rpm for phpMyAdmin, which works quite well.
Why not look at similar projects to phpMyAdmin where it's a single purpose add-on. First try it as a contrib, and then, with the authors permission, write a e-smith manager plugin.
Remember, it's Microsoft's strategy to divide and conquer...
Craig Foster