Magento 1.7 – How to Remove Discount and Grand Total from Cart Total Page

If you defined somewhere (not in the cart rules) free shipping, there is no way to change this (I would guess).

But if you defined free shipping via cart rule, you can define a new rule, which is higher prioritized, check if it matches and then just stop processing (Stop further rules processing)

There are currently a few things odd with the information you have posted. You stated that you want to address the cart total and order total. Your observer sales_order_save_after will fire every time the order is changed (for example when the order is shipped) and I would say too late for your scenario.

Your code does not make use of the observed event at all. I would expect to see something like

$obj->getEvent()->getOrder();

Overall I suggest you revisit your current approach and implement it via a custom total - see this great introduction on how totals work in Magento by Classy Llama or at least use an event that is more targetted like sales_quote_collect_totals_after or sales_model_service_quote_submit_before.