Misery's End seems to be the odd one out in this case. Assassinate on ninja has a pretty hefty cooldown by comparison too. I wouldn't mind if all the longer ones got a reduced cooldown, but I would think it would be more balanced, and an easier adjustment, if they just increased the one short one.
I'm thinking for other times you know you're going to take damage but there is no cast bar to look at, like the stack in O2s, or after the second sword in Susano EX, it becomes guesswork as to when you should pop Third Eye. Whereas other jobs with defensive cool downs get a longer time to take advantage of the mitigation effect, Samurai needs to time it perfectly to not only take less damage, but to proc that move/heal. Only fight without a cast bar I've managed to get it right every time so far is beginning of the second phase in Shinryu EX.
Taking it into comparison, Riddle of Earth has a 30 second duration to get a reduced damage and refresh greased lightning, and Shade Shift has a 20 second duration. I feel like just to make it balanced with other similar DPS actions, it should have a slightly longer duration.