I don't know the extent of the problem but taking down an online service for weeks is very uncommon. I guess (speculating a bit) that Apple could have applied a quick fix to the problem within a day to save their (short term, at least) brand appearance. I think "just getting it secure enough" is the most many people would do if an important service was down. It appears that Apple took the time required to deploy a proper fix, prioritising security over shot term wins.
It would be interesting to see what someone like Microsoft or Amazon would have done in this situation, or what Apple would have done if it was all of iTunes instead of the dev centre.