The Hanso Foundation's actions are aimed at preserving humanity. They are attempting to counter act the Valenzetti equations' foretold end of man. "Evil" acts may be required in order to preserve the future for all of us.
"The needs of the many outweigh the needs of the few." This could possibly be the Hanso Foundation's modus operandi.
According to The Fall of DHARMA theory The Hanso Foundation never canceled the DHARMA Initiative, it eliminated it in a massacre. The Hanso Foundation made a mistake trusting the Rebellion's "Eye Witnesses" who claimed it was DHARMA who had rebelled against them. The Hanso Foundation was forced to cover this up to prevent it's reputation being shattered and this is what Rachel Blake is trying to expose. Some DHARMA members survived and these are the Others.