It will still protect against anything short of a determined attacker with direct access to the hardware for an extended period.
Very little is secure against such a scenario, even less so if the attacker don't care about the defender knowing after the fact.
But all too often security research seems to consider anything that can be broken, even with the most complicated and time intensive of processes, as insecure.
That's basically the whole point of security research - to find any weaknesses and try to fix them. It sounds great on the surface, but the logical conclusion of reaching "ultimate security" is not so pleasant...
Interesting that Apple already fixed this in iOS 9. Makes me wonder what kinds of crazy tests their security team must be doing, that they can mitigate such things.
What's novel here is just how cheaply they're able to carry out these side-channel attacks.
[2] http://cr.yp.to/highspeed/coolnacl-20120725.pdf -- see section 3, Core security features and their impact
FWIW, there is no publicly known SHA1 collision yet. There's a known freestart collision, and a real world (non-freestart) collision is expected to be found within the next couple of months by the same group (the search is already running on their cluster - and the expected time to success is a couple of months). They have already found the first pair that they need out of two.