I hope this is one of those "lost in translation" things, because otherwise I fear for that group of supposed experts.
The energy amount the rocket impacts with is dominated by its speed, not its mass. A small, fast-travelling projectile can make a hole in just about any kind of armour. The terminal velocity is quite low, but that's in part because of the way it is engineered — an ICBM would probably be able to put a hole through a ship deck with ease.
There is a lot of reasoning by analogy vs. reasoning from first principles going on, and the latter seems to be winning. But the main driver of the space industry is governmental funding, not commercial. Much of those statements were probably political; SpaceX have prevailed, and indeed found some champions of their own (John McCain is rabidly behind them, and some of the statements he comes up with are ludicrous in their own right, for example), though not before enduring some setbacks.
While what you've said is true, in practice it isn't a problem.
If the F9 first stage is out of control and going too fast, it will almost certainly miss the barge to begin with. The barge is small, the ocean is big, and the F9 has to maneuver very precisely to reach it.
If it does reach the barge, it will likely be moving relatively slow, and thus is less likely to sink the barge, even it things go crazy at the last moment.
1/2m * v^2
Either way, the relative masses matter. It takes a lot more effort to punch a hole through something much more massive than your projectile! It doesn't make much sense that a light, nearly spent rocket stage would punch all the way through a massive barge. And even if it did, the hole still wouldn't be big enough to sink it.
Would any "expert" really believe SpaceX didn't run the numbers millions of times, and do millions of simulations to confirm they could slow it down before actually spending the money to buy and outfit drone ships, build landing legs onto their rockets, etc. etc. ?
I mean, honestly, while the devil is in the details for an actual landing, they must have been pretty damn sure they could at least slow the thing down sufficiently.
There are several orders of magnitude there.
When shot with a rocket all the air leaks out of the steel barge.