Aside from the fact that SD cards are actually available in a lot of temperature ranges I'd call "industrial", for devices where an vibration means that spring-fastened connectors won't do: eMMC, soldered to the board is pretty much a drop-in replacement, if your device supports both SD and eMMCs (and the Zynqs do, IIRC).
If you need interchangeability of storage media, but need to be vibration-resistant: tough problem. I'd guess my solution would probably be eMMC on a carrier board, connected via some appropriately rated connector (and/or secured using machine screws). Alternatives include booting from SPI flash (sloooow) and/or eMMC soldered onto the same board as the Zynq, and as soon as you have Linux (or even just uboot) running doing whatever your hardware supports: PCIe/NVMe, SATA or SAS (if you can load an FPGA image, why not?), USB, network...