I've gotta tell you, I don't see how talking about "proofs" of the CT or ECT adds any light to this discussion. Such "proofs" tend to be exactly as good as the assumptions they rest on---in other words, as what they take words like "computation" or "efficient computation" to mean. So then why not proceed right away to a discussion of the assumptions, and dispense with the word "proof"?
That much was clear already with the original CT, but it's even clearer with ECT---since not only is the ECT "philosophically unprovable," but today it's widely believed to be false! To me, quantum computing is the huge, glaring counterexample that ought to be the starting point for any modern discussion about the ECT, not something shunted off to the side. Yet the paper by Dershowitz and Falkovich doesn't even touch on QC until the last paragraph:
The above result does not cover large-scale parallel computation, such as quantum computation, as it posits that there is a fixed bound on the degree of parallelism, with the number of critical terms fixed by the algorithm. The question of relatively [sic] complexity of parallel models will be pursued in the near future.
I found the above highly misleading: QC is not a "parallel model" in any conventional sense. In quantum mechanics, there's no direct communication between the "parallel processes"---only interference of amplitudes---but it's also easy to generate an exponential number of "parallel processes." (Indeed, one could think of every physical system in the universe as doing so as we speak!) In any case, whatever you think about the interpretation of quantum mechanics (or even its truth or falsehood), it's clear that it requires a separate discussion!
Now, on to your (interesting) questions!
No, I don't know of any convincing counterexample to the ECT other than quantum computing. In other words, if quantum mechanics had been false (in a way that still kept the universe more "digital" than "analog" at the Planck scale---see below), then the ECT as I understand it still wouldn't be "provable" (since it would still depend on empirical facts about what's efficiently computable in the physical world), but it would be a good working hypothesis.
Randomization probably doesn't challenge the ECT as it's conventionally understood, because of the strong evidence today that P=BPP. (Though note that, if you're interested in settings other than language decision problems---for example, relational problems, decision trees, or communication complexity---then randomization provably can make a huge difference. And those settings are perfectly reasonable ones to talk about; they're just not the ones people typically have in mind when they discuss the ECT.)
The other class of "counterexamples" to the ECT that's often brought up involves analog or "hyper" computing. My own view is that, on our best current understanding of physics, analog computing and hypercomputing cannot scale, and the reason why they can't, ironically, is quantum mechanics! In particular, while we don't yet have a quantum theory of gravity, what's known today suggests that there are fundamental obstacles to running more than about 1043 computation steps per second, or resolving distances smaller than about 10-33 cm.
Finally, if you want to assume out of discussion anything that might be a plausible or interesting challenge to the ECT, and only allow serial, discrete, deterministic computation, then I agree with Dershowitz and Falkovich that the ECT holds! :-) But even there, it's hard to imagine a "formal proof" increasing my confidence in that statement -- the real issue, again, is just what we take words like "serial", "discrete", and "deterministic" to mean.
As for your last question:
Quantum computing would be a likely counterexample, if in fact it can be instantiated, but are there possibilities "weaker" than quantum that would be counterexamples as well?
Today, there are lots of interesting examples of physical systems that seem able to implement some of quantum computing, but not all of it (yielding complexity classes that might be intermediate between BPP and BQP). Furthermore, many of these systems might be easier to realize than a full universal QC. See for example this paper by Bremner, Jozsa, and Shepherd, or this one by Arkhipov and myself.