At the end of Captain America: Winter Soldier, three helicarriers are about to go into the air. When they're activated, they will line up the targets on twenty million people identified as dissidents and execute them, allowing Hydra's 'New World Order' to be realized.
"Despite all diplomacy and the handshaking and the rhetoric, to build a better world sometimes means having to tear the old one down. And that makes enemies." -Alexander Pierce, CA:TWS
We all know Steve was on that list; we learned from this deleted scene that Natasha was not:
"Your loyalties are negotiable. Hydra does not fear those they can buy."
Where does that leave Pierce? He certainly seems loyal. He spends his dying breath whispering "Hail Hydra". Why would he be on the list of targets for Project Insight?
Because Insight targets people who are threats "now, and in the future."
Pierce has grown powerful. He's proven that he's willing to act against those he respects (he's gone behind Fury's back for years). While he's loyal to the principles of Hydra as he knows them, there's no reason to assume that those principles will remain the same. In the 40s, led by the Red Skull, Hydra was part of the Nazi science division, and it's clear that by 2014 their ideals have shifted (they're still terrible, no question).
The two men pulling the switch on the Insight targets were on the list.
Hydra were willing to sacrifice Howard Stark, despite his brilliance, to achieve their goals. It stands to reason they'd be willing to sacrifice Pierce as well. For the greater good.
But that's not even the kicker.
He would have had access to the list. It would have been necessary for someone to double-check and make sure it was accurate, that there weren't any sacrifices being made unnecessarily.
"I can bring order to the lives of seven billion people by sacrificing twenty million. It's the next step, Nick, if you have the courage to take it." -Alexander Pierce, CA:TWS
He made the choice to go down with the Helicarriers. Because he believed that it was the right thing to do.