It will be okay to use the MAX5965A in conjunction with a simple LDO like the MAX6765 as configured in the MAX5890EVKIT datasheet. Please follow these steps to do so:
Connect DGND and VEE together so that both are both -48V. Now AGND is 48V above VEE so AGND and DGND are different. Now you can put VEE into the GND pin of the LDO (MAX6765) and your output of that chip can be configured to be 3.3V above VEE. Since everything is referenced to VEE, and the Abs Max ratings section shows that VDD can be anywhere from -0.3 to +80V above VEE=DGND=-48V, you will be okay.