It is not possible until patch 1.31+ (or 1.29.2 with
Warcraft III: Community Edition).
Maybe there are other mods that allow for it, but none that I know of.
Changing abilities or having multiple levels of it and adding to modify it was the only way to do it until actual support was added.
Assuming that it is a hero abilities with multiple levels, you'd need a dummy ability where you put your points, have it hidden and trigger-add the actual ability that has the same level.
Then set the "actual ability" level, and setup the ability multiple times but with different cooldown values.
1-3 - 5% cooldown reduction
4-6 - 10% cooldown reduction
7-9 - 15% cooldown reduction
...
Then set the level of ability to whatever "cooldown reduction". Of course, the actual levels don't matter.
Having too many ability-levels on a lot of abilities can cause map saving to slow down, so if there are many heroes that all need this it can become annoying.