Was it just a once off or do you always need to pull the battery out?
Probably the best thing to do for the days shooting is not to turn the camera off at all. All of the
modern Nikon DSLRs from the D100 onward use very little power when they're in power-on standby - in fact, it's only very slightly more than being powered off from everything I've read. I know I've accidently left my D70 in a bag for 2 weeks turned on, picked it up, and it still had enough charge to take the shots I wanted.
There's been posts on changing lenses with the power on before, so you can probably search it out, but the general consensus was you can change lenses with the power on, but it's probably better to do it with the power off if you can.
The most important thing is if you're taking the battery out to power off the camera, make sure the green CF memory activity light has gone out - you could end up with data corruption otherwise.
You may want to try using the recessed reset button in the bottom of the camera - this will most likely fix the problem - I think this happened to my D70 once and it fixed it. But... if its working well enough, do what you have to, then fiddle with resets and whatever later