It is specifically the village/cantina area of the Desert that will be renovated. But that plaza is still used quite often by visitors so I really don't think they're gonna get rid of that whole area.
Personally, I think they're either going to re-open the Cantina area (I've never seen it open), or they're going to get rid of the restaurant bit and replace it with one or a few new terrariums, or even an open-topped reptile enclosure.
There's multiple Desert reptiles behind the scenes (at least Desert tortoise and Side-blotched lizard), and quite a few more options to add (Chuckwalla, Desert iguana, Zebra-tailed lizard). Burgers' Zoo in general has a bit of a lack in herps (17 species of herps, 8 of which are rarely seen by the general public) so it would be a good opportunity to add more.
Besides, there's not that many mammals available to add in the Desert