JTAG clock speed is controlled by the JTAG pod, not the Zynq. Some allow configuring the speed, others have a fixed value. Note that maximum speed may be limited by your Zynq board design, or the length of JTAG cables.
It is much faster to program flash from Linux (or even from uboot). I would recommend programming just FSBL and uboot via JTAG. Then you can either use network to fetch zImage and a ramdisk, or you can transfer data into RAM (much faster than into flash) and use uboot "sf" command to write it to flash.