"The real issue for me is not the stuff; it’s not the equipment—because we need it. The issue is the way in which we use it—when and how we deploy advanced equipment; when and how our officers are trained to use that equipment. The way we do it matters enormously."

The big factor is the policies of deployment and the warrants that judges sign off on based on the situation - that situations are properly vetted and equipment is deployed to match the situation. In my opinion it sounds like the situation in the OP's article could have been better vetted, but I don't have all the info. It's definitely very alarming when you have a tactical response to a situation as displayed in that article.

If you're using an MRAP to bust down the door to serve a misdemeanor drug warrant, that's a big problem. If you're using it as protection to drive up to a house and rescue a downed officer where a barricaded subject is shooting rounds out the windows and bullets are ricocheting off the vehicle, that's perfect.
If you're using an M79 or M203 launcher to shoot frag grenades at US citizens, that's also a big problem. If you're using that M79/M203 to launch CS gas into a house where a dangerous subject is barricaded, probably not so much of a problem.

We don't want law enforcement using the equipment in situations that don't require it, but at the same time, we don't send our troops facing AK-47's and other rifle rounds in dress pants, a shirt and tie with a gun belt and a simple level III soft armor vest underneath. I'm not saying the US is a war zone, but bad guys often barricade themselves in houses with an AK-47, AR-15 or other rifles. Equipment needs to match the threat; it is when that element is misappropriated that we have a problem. It'd be a big task to find officers willing to hunt down a violent felon (who's made threats to kill law enforcement, with outstanding warrants and who has access to rifle-power firearms) wearing nothing more than their street patrol gear. Rifle threats are very common nowadays. Rifle plates have to be carried in an external tactical carrier, they aren't practical concealed like soft armor is - if deployed properly, it's a lot more comforting to wear against a rifle threat than the soft stuff that will be defeated like butter against any rifle round.