I've just been playing around and you can add the totem name right in you castsequence.

Like so.

/castsequence reset=combat Flame Shock Totem, Flame Shock,,,, Other Totem,,,, ,,,, ,,,, ,,,,

It doesnt catch it all the time, but works pretty good. Only works if you press the button pretty slow though. I was trying 4 presses per second and it would switch it mabye 75% of the time. Switching the totem doesnt trigger the GCD but i think if your in the middle of casting something else when it becomes active it wont switch.

I did notice though you can only have 1 totem effect up at a time though. If the second one procs while the first is going, the first will end. I could still see this being useful though, especially with stuff that has a set number of procs per minute.

Hopefully with some more tweaking it will work better.