It makes sense that if Hydra had infiltrated SHIELD and were secretly trying to achieve their own ends, that they would have several avenues for doing so. Project Insight was Hydra's endgame. Everything they did was leading up to that, but for 70 years they were biding their time, growing in numbers, and achieving their smaller goals. Project Insight only became possible after the events of Avengers. So before that, they used Zola's algorithm on a smaller scale to help them achieve their goals and kill their enemies and potential enemies. We need to remember that the Clairvoyant/Garret wasn't the head of Hydra, * SPOILER * was. And before him, someone else was. So he used various tactics to throw the world into turmoil, to remove threats to Hydra, to gather technology and power, to experiment on people so they could create super soldiers, etc. So they used the Winter Soldier, and Centipede, and the Clairvoyant, and possibly AIM, or the Ten Rings, etc to achieve those goals. While Centipede was using alien tech, extremis, super soldier serum, and deathlock technology to create super soldiers, Strucker was using Loki's sceptre to control or create mutants/"miracles". Hydra is a big organization and has it's tentacles in lots of different things.
I'm sure she looks better out of them. Just saying. 
