Typically, a thermal runaway occurs when a battery gets hot enough to degrade the integrity of the insulating barrier separating two of its adjacent power cells. Which produces a negative earth fault, which further raises the battery's temperature, which provokes a feedback loop of overheating that often as not ends in battery destruction.
It could be evidence of a structural problem with the battery, or of inadequate cooling, or of excessive demands being placed on it. But as this isn't happening with the Caterhams, and being as Adrian Newey has a history of "short-changing" the batteries' cooling needs, I suspect it is a combination of both of the latter. But Renault claims the will have the problem fixed by tomorrow. Which might mean the batteries will be modified to Caterham's detriment (because RBR are the 800-lb gorilla of the Renault camp).
If you're looking for logic in the 2014 engine formula, I am afraid you are on a fool's errand. Because it has nothing to do with competition, or improving the show. Rather it is an act of contrition, the sport evincing its discipleship to The New Green Religion.
I think that to their minds, it is a "proof of concept" with too much riding on it to risk failure. Else they collectively would look foolish, and run the risk of being excommunicated to boot (or at the very least forced to pay some exorbitant penance). Which is the chief reason the task of balancing the allocation of energy reserves (electrical vs petrol) has been removed from the driver's control. Because that singular task is the linchpin of the whole wretched scheme, and is too precarious a balancing act to leave the outcome subject to human error. And also why rules tweaks probably will be shortcoming. They will not let it fail, the sport be damned.