As a grand-old Bitcoin exchange, is it possible for it to ignore a flaw that had been detected in 2011?
Of course it is possible. The fact that it took many other bitcoin services unawares too—look how many other exchanges suspended withdrawals—shows that many people other than those running MtGox failed to anticipate the problem. Even the core developers didn't consider it a priority until someone started using it to attack the network, and that happened
after MtGox had already suspended withdrawals.
Clearly there is something wrong at MtGox.
Clearly their spinning of the malleability issue was unhelpful.
Clearly their inability to put a fix out when others have done so is yet another cause for concern.
Clearly they can manipulate the market by suspending withdrawals of btc of fiat or both and the community just has to trust (!) that they don't succumb to the temptation to do that.
But also clearly they had these sorts of problems long before malleability was in the news, so this is not really anything new and anyone who has an opinion on MtGox is not going to change it now.
Those with funds stuck inside MtGox may want some sort of external investigation to "encourage" the release of funds, but for the rest of us who stopped dealing with MtGox a long time ago I think it would really be best if they died by means of people no longer using them and them fading into irrelevance. That would be a lot less damaging to bitcoin as a whole.