After playing for an hour or so, my fingers start to get really, really sore. Then, when I let go of the controller, they kinda just stay in the same position. It's probably an issue with how I hold the controller (right middle finger on RT, right index finger curled so it can hold the A button while running, and right thumb for camera control on the right stick), but they usually hurt for a few days afterwards. Anyone else have similar issues?

Dude that is just weird. I just have thumb on A and RT with Index and it still hurts. 
 
One thing I hate is that if I am chasing or running and I want to readjust my left thumb, the ezio just stops or the horse just stops.

Seeing how I can't really play the damn thing my answer would be NO!  
 
Great I have a $60 dust collector. 

You hold the controller in a very odd fashion...

I only hold it that way for free-running, but it's the only way I've found that lets me hold RT, A, and the thumbstick at once...

How often do you really need to adjust the camera while free running?  Can't you just normal run for a second whenever you need to fix the camera?

Ive just realised that I hold it in a similar way without realising, however I used my index finger on the stick. 
 
I dont get any problems, so try that?

" Dude that is just weird. I just have thumb on A and RT with Index and it still hurts.  One thing I hate is that if I am chasing or running and I want to readjust my left thumb, the ezio just stops or the horse just stops. "

I don't constantly have my thumb in position to adjust the camera but even so if my hand aches a little after gaming (and it's usually more than an hour) it sorts itself out pretty quickly. I think you need to be a little careful! This is an odd question but it just came to me! Are your hands getting cold?! You see I'm often wearing fingerless gloves when I'm gaming because my hands are freakishly cold and can get all stiff if I play too long without them!

I never felt like I needed to be able to control the camera while sprinting. If I did, I'd just quickly let go of the A button to move the camera to the right position. 
I do still get stiff fingers after holding down the trigger for far too long. Though, it only lasts for a few seconds. 
It probably has to do with me holding the trigger down really hard during the intense moments in the game.

" You see I'm often wearing fingerless gloves when I'm gaming because my hands are freakishly cold and can get all stiff if I play too long without them! "

" I don't constantly have my thumb in position to adjust the camera but even so if my hand aches a little after gaming (and it's usually more than an hour) it sorts itself out pretty quickly."

Basically, this. Although your hand is contorted in a position mine doesn't even want to go in for ten seconds, your hands will get tired no matter what if you play the game for long periods of time. I seriously recommend not doing this to your hands, though; find a better way to use the thumbstick. Honestly, using your knuckle or palm to turn the camera left or right is going to be much healthier for your hands, and my first instinct, as someone else said, is simply to use the standard run instead of sprint to turn the camera.

Also clicking the right stick swings the camera around behind Ezio so that could be a quicker way to adjust the camera.  I don't feel the need to mess with the camera while free running.  I feel that it does a good enough job of adjusting itself.

How are you holding that controller ? Sounds like a painful game of twister

" After playing for an hour or so, my fingers start to get really, really sore. Then, when I let go of the controller, they kinda just stay in the same position. It's probably an issue with how I hold the controller (right middle finger on RT, right index finger curled so it can hold the A button while running, and right thumb for camera control on the right stick), but they usually hurt for a few days afterwards. Anyone else have similar issues? "

" Ive just realised that I hold it in a similar way without realising, however I used my index finger on the stick.   I dont get any problems, so try that? "

Why do you hold the controller like that O.o I just hold it the same I do in every other game.

" Also clicking the right stick swings the camera around behind Ezio so that could be a quicker way to adjust the camera.  I don't feel the need to mess with the camera while free running.  I feel that it does a good enough job of adjusting itself. "

No, I've been holding the controller like you described for years. Not all the time of course, but in certain instances where it makes sense. I kind of automatically started doing that back with Halo 2 because it was very useful during melee fights (B was the punch button, and being able to look around while punching often gave you the upper hand).
 
As for this being useful in AC:B, I certainly think so. While you can easily get away with just switching between A and RT in single player, those few seconds you stop sprinting can very well mean death/loss of target in a multi player chase.

Get an arcade stick lmao. It might help.

That's your body's way of telling you to stop holding the controller like an idiot.  Seriously, why would you ever want to do that?