Hi @jhughesWSESD,
I think you're probably already going town the right path for this: working with your SIS vendor and Instructure to get that integration smoothed out.
I dabble in some "short code, high impact" customizations via CSS and JS, and it's definitely possible to do a lot of things. This particular one, however, would be complex because not only are there UI elements to change the status to excused (probably easy-ish to hide those), but teachers can type out EX in the gradebook or speedgrader to apply that status as well, and I think that would be much more complex to catch/block.
Hope this helps a bit!
-Chris