You can try to raise the priority of your css rules by some simply tricks.
For example, you can give an id attribute to your most external container element in the html, for example id="yourContainerId". Then you can raise the priority of your css classes by prepending #yourContainerId to all your classes that you want to raise:
#yourContainerId .yourClass1 {
}
#yourContainerId .yourClass2 {
}
etc..
if you want to know more about css priority, this is a good resource: http://www.w3.org/wiki/CSS/Training/Priority_level_of_selector
Note: this trick cannot work in some particular conditions, because if your javascript writes inline style on your html elements there is nothing to do, you can only remove them with js. Tell me if you need a jsFiddle example