I just talked with a wilderness person from Yosemite about permits and he mentioned there has been bear incidents at Thousand Island Lake including a bear ripping up a tent. Thus they are advising to avoid camping there.
Bears have been more active this year along the trail since the berries are not as plentiful and thus human food is easier to get.
Elsewhere I read that camping at the TM campground voids your JMT wilderness permit since you are camping outside of the wilderness.
Additionally both Cathedral Lakes are open for camping.
-martin
OregonBeerMan