Well, it depends somewhat on if you have access to the plumbing below or not. Setting a toilet isn't all that hard, but when it's not done right, you can get issues like you have now - it leaks, smells bad, and can rot the floor. If the flange sits too high after taking out the tile, you may not be able to get the toilet to sit and seal properly on the flange unless you make a big shim underneath it to raise it temporarily should you need to continue to use the toilet in the interim. If you have access to the plumbing below, it shouldn't be too hard to cut off, and then raise a new flange to the proper height after your remodeling has the new floor in. It can be done from above with an inexpensive, internal pipe cutter.