So I got annoyed at reading all the armchair pilots' responses and skipped a few posts, therefore forgive me if it has been said already.
All the comments coming from them suggesting an engine shutdown should have been made on shortfinals is the dumbest thing in that scenario I can think off. It's obvious both engines had ENG CTL SYS FAULT's.
From the report it states that they stopped within a short distance of the upwind threshold. They also were able to select maximum reverse until the aircraft came to a stop and the engine remained at 70% N1. I wonder what would have been the stopping distance had they shut down the engine. Even if they went of the runway by 10 meters that would have put a serious bent in the nose wheel structure and I'm pretty sure a bent nose wheel is a lot more expensive than a few blown tires. Imagine how they would have been criticized by the same armchair pilots if they did shut the engine down and bent the frame! (Read the following with a Homer Simpson armchairpilot voice) "Well maybe the engine was stuck at 70% N1 but they still would have had reverse and been able to stop within the remaining tarmac, DUHHH"
I know economics and airline budgets were the last thing on their minds during approach but surely having control of the aircraft and at least one engine running while racing towards the tarmac over water still, albeit at 230kts, is very reassuring still. Who cares about FCOM 1 explaining tire limit speeds in a situation like that!!?? C'monn!!!
In conclusion, having shut the remaining engine down would have been unwise. They made excellent decisions and can not be criticized in the least. No board of inquiry will question their actions - this is not the air force.