As a slight aside: I've been arguing recently that we should use moral theories that are not universally applicable, but have better results than existing universal theories when they are applicable.

In this case, you correctly point out that many moral theories have conflicts between their evaluation of the value of past lives (possibly negative) and their valuation of present existence (positive). Personally, I answer this by saying my moral theory doesn't need to make counterfactual choices about things in the past. It's enough that it be consistent about the future. I think that's a plausible answer, here, to the question of whether "my existence justifies the past suffering of my ancestors".