The commission is tasked by the council to translate policy into proposals. If the council directs the commission to repeal a law, they will draft a proposal to do so. The council also appoints the head of the commission, who has final say in the members. The council in turn is composed of the heads of state of the EU members, so it is mostly directly elected.

Maybe people just need to take more care which leaders they elect, if they don't like the policies that result from it.