I believe the problem is actually caused by the fact that for <circle> elements, Apple makes the origin of the stroke at a completely different spot than all the other browsers. It has nothing to do with rotation or a bug in GSAP. It's just an annoying choice Apple made. You can resolve it by converting the <circle> to a <path> so that the coordinates are explicit about where to start. MorphSVGPlugin has a super convenient method for doing this, so all you'd need to do is add this line to the top of your JS:
But I noticed you're not a Club GreenSock member, so you don't have access to MorphSVGPlugin. I ran the conversion for you and got this, which you can just swap in for your <circle> instead (thus you wouldn't need MorphSVGPlugin):
<path class="st2" id="progress" d="M589,319 C589,468.1,468.1,589,319,589,169.9,589,49,468.1,49,319,49,169.9,169.9,49,319,49,468.1,49,589,169.9,589,319z"></path>
Does that help?