Well, if you figure that the rehab is going to take 7 or 8 months, you're going to impact a lot of folks regardless. By timing the rehab to start just after Easter, and be finished by the Christmas season, Disney is obviously indicating the importance of capturing spring break and December crowds, at the expense of summer crowds. Otherwise, Disney would have started the rehab right about now, and finished up around August. That would have blown all the spring break crowds, and gotten SM ready just in time for the slow-ish season (Aug-Sept).
For shorter duration rehabs, it makes good sense to do them in the Jan-Feb, September-October timeframe. However, that's also a prime time for other rides to go down for regular maintenance, so you run into a problem with having too few of your big-ticket attractions open.
The POTC rehab in 2006 was from March-Jun, if I remember. Probably not the best timing, but I wonder if that whole project was a rush job, given a late greenlight, and an immovable deadline of being complete in time for the premiere of the second movie. The HM rehab in 2007 is more puzzling, going from June until September, basically missing the entire summer season (but opening in time for the Halloween season and
MNSSHP). I would think it would have made more sense to do the HM rehab a little earlier (say, start right after Spring Break season ended in April), but I'm sure Disney had some logic on that scheduling.