Thanks for the help everyone.
After some fiddling, it became evident that applying -ms-overflow-style: none to the body or html completely eliminated all the scrollbars in IE. But armed with this knowledge, I was able to make a change to the script that gets it working in IE without any issues:
// in some browsers (like certain flavors of Android), the getScreenCTM() matrix is contaminated by the scroll position. We can run some logic here to detect that condition, but we ended up not needing this because we found another workaround using getBoundingClientRect().
div.style.cssText = "width:100px;height:100px;overflow:scroll";
parent.style.setAttribute('-ms-overflow-style', 'none');
parent.appendChild(div);
div.appendChild(svg);
point = svg.createSVGPoint().matrixTransform(svg.getScreenCTM());
e1 = point.y;
div.scrollTop = 100;
point.x = point.y = 0;
point = point.matrixTransform(svg.getScreenCTM());
_svgScrollOffset = (e1 - point.y < 100.1) ? 0 : e1 - point.y - 150;
div.removeChild(svg);
parent.removeChild(div);
parent.style.setAttribute('-ms-overflow-style', '');
I am marking the answer solved, but it would likely be good to have something like this included for those who want the page to have scrollbars in IE. Perhaps with some conditional logic to apply this css change only if its IE.