First you'll need to browse to where the themes are stored, so you'll need to to var/stasth/themes.xXxxxXxX (random numbers/letters). Here you can see all themes downloaded from Cydia (you can also add/remove theme from here via SSH easily).
Next find the theme you're looking change the wallpaper of, and look for a file called "wallpaper.png" or "wallpaper@2x.png" and likewise for the lockscreen. You can simply delete these files and respring and you'll have your default iOS wallpaper which you can change using the normal way in the photos/settings app or whatever
Alternatively you could replace the image file for one you wanted, as long as you name it the same
You can use this same method to modify/delete any parts of themes really, like icons (stored in the bundles section of a theme) or just UI images (stored in the UIImages folder

).