I found it in the kernel sources, and it's controlled by a device attribute at /sys/devices/platform/mxcintuart.0/uart_clk_state. Set it to 0, and it won't gate.
I was about to write an init.d script to do that for me, but I found something in /etc/init.d/power that does that for you. You just need to create a file called DO_NOT_KILL_UART in /mnt/us.
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