drMerry - re your "feature request" - you can do this already by applying a search restriction before you do your duplicate search. So come up with a search that covers all the stuff you want to exempt, for reuse puposes save that as a saved search, set it as the search restriction and you should be good to go.
Re your other problem. Memory usage during "normal" comparisons isn't an issue. I suspect what you have done however is created an enormous exemption group. How many members did it have in it? That is something we may need to think of a more optimal storage strategy for, because you end up with some kind of logarithmic or exponential storage problem if your groups starting having hundreds (or more) members in that you try to exempt.