Use a "2 ability" way, one based on Wind Walk, the second an instant dummy ability called, let's say Cancel Invisibility (put it just up from the Wind Walk one on the unit info card).
If the unit is a hero, you should add the dummy ability once Wind Walk is learned (otherwise give it directly to units that have the Wind Walk).
The effect of the ability should be removing the wind walk buff. Simple. You can make the dummy ability be based on Berserk so it doesn't interfere with the orders of the unit. You could potentially make it based on an auto-cast ability, ie. Frenzy, so the auto cast order makes the unit cancel the invisibility.
A custom cooldown can be possible too. My guess is this (don't know if it is the only possible way tho): you are basically using a spell effect event, in which you remove the casted ability, add a dummy ability with the same icon, tooltips, X/Y position, with the cooldown desired, and of course 0 mana cost, then issue the order of the dummy unit, and finally start a timer that after it's expiration will remove the dummy ability and will add the normal ability (reverse effect). Complex. If you need this ability to be MUI you will need either a looping timer to track all instances or simply one timer per unit. In general this approach only works properly if either 1. all unit's from the system have 0.00 cast point (best approach), 2. you're basing the dummy ability in a 0 cast point ability, like indeed Berserk/Fan of Knives. Otherwise players can just issue stop.