I don't think barefoot running is inherently bad for you long term or anything, I've had friends do 80+ mpw, including trail/gravel running in vibrams with no problem. Those guys/gals are < 140 lbs with impeccable form though.
I think barefoot running can be an amazing way to "teach" people the correct way to run, but for most people, they should take that form and move it over to a shoe that does have a bit of impulse reduction. There are many steps between vibrams and super cushy shoes.
Look for something with a low heel toe drop/offset (I'm at 4mm right now) so that your heel isn't forced to land before your midfoot. Racing flats are gonna be just a step up from vibrams, then you get into shoes like the Saucony Kinvara, which remove some durability from the heel (which doesn't really matter as you're landing on your forefoot) to reduce weight but still have padding.
Running shouldn't hurt anything other than your pride. If you're feeling pain, don't run. Don't be scared about going to your local shoe store and having them show you what's up. Happy trails.