I have this problem with themes too, and the solution is simple. Take the theme that you are going to install, open the zip, and just remove the apps, fonts, or framework you don't want altered.
For example, I despise the font changes alot of themes force on you. Makes my twitter streams unreadable, so I just open the zip, and delete the fonts folder. That way it won't override the stock fonts. I've never tried deleting individual files, but that method should work for icons as well.
Just open the framework.res (rename the .res to .zip or .rar if you have WINRAR installed, or just use the "open with or choose default program" option) goto the res folder, then drawable-hdpi and just delete the battery images from the folder before you install the theme.
An easy way to do this, is to make a copy of the zip first so you'll have a proper version of the theme to view. Open it up with winzip, WINRAR or whatever archiving tool you use on your computer. Then browse the files in thumbnail view to find the images you want to get rid of. Make a note of their file names, then open up the other zip, locate the files in question, right click, delete em.