Either override templates to change thumbnails: http://docs.woothemes.com/document/template-structure/
OR (better) use the filters:
woocommerce_in_cart_product_thumbnail
and actions:
remove_action( 'woocommerce_before_shop_loop_item_title', 'woocommerce_template_loop_product_thumbnail', 10 );
Once thats removed you can hook in your own action function.