I would be in support of keeping the pvp cool down, I feel like it makes pvp more interesting, for lack of a better word, and requires more skill as there is a lot more variables, including the cool down.
I get that you're thinking of this from a purely pvp point of view, but changing the cool down would effect other aspects in the survival mechanics of the server. Pve for example would become all about jitter clicking again instead of waiting for the right moment to damage them.
You also have to remember, while it'll work well in a 1.9 pvp server, it mightnt work as well in a 1.9 survival server as they attract different kinds of players.
How would turning it off work? Would it reverse all of what 1.9 did to pvp, or would it only remove the cooldown? Assuming it only removes the cooldown, and with it the special abilities, axes become a lot more over powered as they are now stronger then swords, a larger cooldown was to balance this.
Personally I don't believe it would suit the server itself to turn pvp cooldown off