iOS 6 WebKit now provides support for file input elements. When choosing a 'file' it allows you to choose a saved photo from the photo library on the device or take a new photo if the device has a camera. iOS doesn't automatically orient photos taken with the camera, but instead stores orientation metadata in the photo that can be accessed in order to orient the photo properly.
So this bug is more a mismatch with user expectations. If a photo has been chosen with a file input and you are accessing that photo through the DOM with JavaScript and drawing it to a canvas, the photo will not respect the orientation metadata and you have to do it yourself.
<script src="http://www.nihilogic.dk/labs/exif/exif.js"></script>
<script src="http://www.nihilogic.dk/labs/binaryajax/binaryajax.js"></script>
<input type="file" capture="camera" accept="image/*">
<p>The image appended to the body</p>
<div class="append"></div>
<p>The image drawn to a <canvas></p>
<canvas id="normalCanvas"></canvas>
<p>The image drawn to a <canvas> with orientation correction</p>
<canvas id="correctedCanvas"></canvas>