The bitcoin network does over 3 quintillion (>3,000,000 trillion) hashes a second. So even if they were doing a significantly harder to compute hash -- they're still only a very small part of the computational power the bitcoin network is using.
So it's probably already more effective to attack wallets than join a mining pool.
Ed: Estimate of numbers --
Assuming that their hashrate was over 3 months (article says nearly a year, but they're also scaling), they had about 300 million hashes per second. Bitcoin had 3 million trillion hashes per second over the same period. So you're talking 1 to 10 billion in raw hashrate, and even with a generous challenge factor, bitcoin is using millions of times more compute power.
There were about 150 thousand bitcoins mined over that period, so 1 in 10 billion of that is 0.000015BTC.
Since they hit 3 in use accounts with the same compute effort, they almost certainly made more BTC attacking wallets with collisions.
Ed2: How much parasitic hashing --
If you figure the average active wallet has between 1 and 5 BTC (very high variance), and the wallet hash takes about 100x as long (over estimate), they made 3-15BTC vs 0.015BTC by attacking the network versus mining, or about 200-1000x as much.
Since colliders are themselves unlikely to collide (and thus competition doesn't starve out colliders), the system will only stabilize if 99%+ of miners drop out of the pool or the difficulty in finding a collision raises 1000x.
Given the sunk costs in dedicated mining rigs and that new hashes would be breaking, it seems like parasitic hashing will continue to be an issue.
On the plus side, only a one-in-a-million chance it wipes one of your accounts.
(Of course, a fluke collision with a high value account might create other problems.)