I think they knew all along that it would take longer than they originally announced. Perhaps it was a case like we're now seeing with Space Mountain: Disney says it will open in November, but all the insiders say it will take a least a few extra months. In the case of SSe, they managed to get away with it; the touchscreen made up the time lst by the curtained-off effects. With Space Mountain, if they go ahead and replace track, they're not going to be able to open a half-baked attraction; it's all or nothing. In any case, I still think Disney knew well ahead of time that it would take longer than they orignally announced to complete the refurbishment.
Reopening the geosphere for the Christmas period was acceptable. They needed the capacity in the park and the ride was incomplete yet passable (for a short time). There was no good reason for Ops to not let WDI take the ride down from January until Easter (which was in late March) to finish the job right and on-time. The original press release even said the total refurbishment time would take several months longer (concluding mid-February I think) than the original closure dates made it seem (which were July 9 - November 1, 2007, then extended to November 14, I remember). there's no good reasonwhy this is still being worked on, and in the third shift no less.
Of course, it's not the end of the world or anything, but they'd save money and have a better product if the company would stop dancing around these decisions and just do things the right way the first time. then we'd have better attracvtions and a little more money in the budget to play with new toys (or at least keep the old ones in working order.)