Your method is absolutely correct. There is nothing intrinsically wrong with using percentages greater than 100%. Percentage is just another way of writing a fraction with a denominator of 100. Just as you can have an improper fraction, (4/3) so you can have something like an "Improper Percentage" as well.
Think about how Google's Android Market can grow by 861.5% in year-over-year revenue, just to pick one example. It basically means that every year Google's Android Market's growth becomes 961.5/100 times the growth of the previous year.
Now to solve your case, we take a simpler example. Let A be 100 and B be 10. Now we need to find how much higher is A when compared to B.
We continue with finding A-B = 100-10 =>90. Now when we express this in percentage we get (A-B/B)*100 that is 900%.
Now let's verify this. What is 900% of B. It's 9B. Now when you add 9B and B you get 10B which is A.
So to conclude, a percentage higher than 100 is alright.