Having used this power, some tips to counter......
First of all think of it like an expose, if you see sparks from the weapon.....GET TO COVER (or run). Too many times have I seen players sitting there waiting for it to wear off.
Next, your weapons don't work but you abilities do, always try to have an ability in your kit bag that doesn't need a weapon.
The Kits this power comes with (usually mines/explosives below Commander) has no other offensive capabilities. DON'T run towards the engineer to melee, as he's probably dumped mines down in front of him.
So best fix, is an Engineers 'Quick Fix' ability. Engineers always carry a few kits with you to adapt and survive.
Weapons Malfunction can continually take one player out (once buffed) from inflicting RANGED damage (important bit that). The ideal target is a Tac Officer (because many of them just seem to charge the enemy, just my impression mind you ). However thats the Engineers offensive ability gone doing that. All he can then do is attempt to grind down the enemy just using the basic damage offered by the weapon (thats why all Engineer fear the Doc). Each Class works in a 'rock, sissors, paper' mechcanic.
Klingon Engineers use this kit more than any other, as they have no access to the 'Bunker Kit' (more favored by the Feds). Now before any whines about Engineers and Docs dominating the match, they have no abilities to buff the ground weapon damage (thats a Tac Officers main ability). Tac Officers, If you meet a Doc/Engineer solo then 'if' the Engineer has the right Kit, and 'if' the Doc has the right Kit. Then if might be a good idea to simply run. The damage abilites offered by these 'nerf/heal' kits are pretty abismal. HOWEVER, they can nerf/heal enough to make it a looonnnnggggg fight (usually goes down to who gets the expose/exploit combo first). No-one can take down a player faster than a Tac Officer. But they can't do it alone/solo, so be aware of freindly Docs and Engineers defences for the win.
...and finally the best tip 'EVAH' for ground PvP. DON'T be afraid to run, play smart and pick your fights (don't let the enemy pick it for you). Weapon Malfunction doesn't need ner***e, it just means players have to adapt a bit more than just pressing the 'pew pew' button.