While I admittedly haven't played in a while (but was considering making a return :P), Golden Wrench was always a way to minimize the necessary manpower on the (frankly boring) MCT repair job so that your teammates can fend off the attackers. You should also keep in mind that arty and V2 unlike Reborn counterparts can and will wreck the personnel inside the structure which made repairing with tool alone pretty unfeasable (exceptioins are RD and CY) if you are dealing with more than 1 of them at the time.
So now you'd have to also nerf artillery units in some way, and last time I checked they weren't exactly OP.
Another thing is general "game philosophy" if you wish. APB is for the matter of fact more of "high risk - high reward" game. You want to kill the building but there's somebody inside? Well, go in and kill that person/people, and structure will fall in a matter of seconds. You don't want/can't? Well, hope that either someone else will or that your enemy's economy is broken enough they won't be able to afford an engie.
Attack doesn't "deserve" to succeed just because there're more of the attackers than the defenders in base at the time, and Wrench helps exactly that case.