I think you'd be asking for trouble if you don't replace the flange. Mixing new parts with the old, rusty flange would not be wise in my opinion. Of course it is tempting because of the work involved, but any kind of patch job would be suspect. I would suggest you consider a professional plumber to do this. It may very well be possible he will have the know how to do the job with a minimal amount of damage to the ceiling below and get the new flange up to the proper height and level. I realize this would not be inexpensive, but this is a job that once done right will last virtually forever and look good as well. I am an avid DIYer, but I have come to realize that there comes a point for all of us where we have reached the limits of our abilities and calling for professional help is called for.