Yes gtk3 can implement css for styling http://developer.gnome.org/gtk3/3.0/GtkCssProvider.html
. As this is cascading there is a hierarchy where the more specialised instances (e.g. css provided in your code for just your program) have precedence over the more general (e.g. those defined by your OS's themes).
Note however that even though you won't break the style of your OS by using gtkcssprovider, it will mean that your program's appearance is not consistent with the rest of the desktop environment. Probably not that big a deal as the rest of the desktop environment isn't necessarily self consistent anyway. One thing to watch out for is to try and not change style issues that tend to vary between platforms and OS's. e.g. netbooks and desktops ideally should have differently styled environments and if you set any of these particular style then you lose the ability for this to automatically vary for your program on the environment level.