I don't suppose you're able to add an extra column on to the table(s) in question, are you?
If so, you could run a pre-compare step which rather than building up a where clause, fills in the values of a bit column on the table marking them as to be included / excluded, at which point your where clause becomes quite nice and simple
. You could exclude that column from the comparison, of course.
It feels a bit nasty, and obviously I realise you might not be able to do this, but it would mean the comparison would only pull back the rows you want to include...