Investigate taking out a travel insurance policy, which "should" take care of the excess payable if something happens to the vehicle, and will avoid you having to pay an additional daily fee. It will also cover things like lost baggage, delayed flights ... but make sure it does cover the excess on the hire vehicle.
Most people now travel via Lasseter Hwy and Luritja Rd, although it means you have to double back a little when travelling to Uluru. If you're not experienced at driving on unsealed and remote roads, that would be the recommended option... and correct, most hire cars aren't covered for insurance on the Mereenie Loop. Please use a map and don't rely on SatNav!!! as happened to some friends of mine.
If you are going to walk the Giles Track, remember you will need to carry all of your water. And there is no mobile phone reception at Kings Canyon, last time I was there anyway. (4 yrs) The rim walk itself is well-signed and there will be plenty of people around at that time of year.
Stock up on your supplies before leaving Alice Springs - anything at Kings Canyon/Uluru is VERY expensive. And take a fly net.
If you are crossing into school holiday time, may be best to pre-book campsites at these destinations.
I would also highly recommend a couple more days with a trip from Alice Springs through the Western MacDonnells, on Larapinta Drive, as far as Glen Helen. I could not recommend that trip highly enough, it's stunning and Glen Helen is a lovely place to stay.
On your last morning, visit Olive Pink Botanic Gardens in Alice Springs for a tasty al fresco breakfast