Hi Meg,
Try to think of it this way (the times are an example of course):
he is supposed to be sleeping from 9am-10:30 am, but only sleeps from 9-9:30 and then 10:15-10:30, so technically he slept for 45 minutes right? But like Kate said, he was out of 'action' for a total of 1.5 hours, in which time you were teaching him that it is time to sleep for a certain amount of time and on a certain type of schedule/routine. In essence you are helping him to set his internal body clock that will tell him "from this approximate time to this approximate time, I need to sleep."
THe theory is by keeping them in the nap setting for the remainder of the nap time, even if you don't get them back to sleep, you are still teaching them that eventhough you woke up early from your nap, it is still time to sleep. Some may agree or disagree on whether this actually works of course, so it is up to you. This is also for the baby who wakes up crabby and still tired from their short nap...if he's waking up happy then you go with the flow KWIM?
HTH!