Now I feel really bad for letting the new one live !! You were right.
If Shepard did not spare the Rachni queen on Noveria, the Reapers will artificially construct a Queen thrall in order to control a rachni army. Shepard can choose to spare this artificial queen even if the Commander killed the real queen. This queen will eventually betray Shepard, taking the Rachni Workers War Assets away and decreasing the numerical values of some Alliance fleet War Assets.
http://masseffect.wikia.com/wiki/Rachni