So, more to the point, I tried the same modification you wanted, Zorykos, at one point, and had the same problem. To the best of my experimentation I found that negative values never worked right for me.
A couple very good solutions to the problem involve triggers:
A) Trigger a caster unit to cast a form of something like Inner Fire to give the unit an armor buff of the same duration as the Berserk buff. This solution is a little worse than solution B because it means there will be two separate buffs in the Stat Card for the same ability. However, even Blizzard does that on some rare occasions, so worry not.
B) Add the Mountain Giant's Hardened Skin ability to the unit when Berserk is cast and remove it after the amount of time specified in Berserk. If Berserk is dispellable, you'll probably also need a trigger to occasionally check units of that type to see if they have the Hardened Skin ability when the Berserk buff is gone. Therefore, this solution is a little worse than the buff solution, which would be dispelled whenever the Berserk was dispelled automatically without a check. It also shows the Hardened Skin ability in the Command Card. If that's a problem for you, it can be solved.