I'd say about 50/50. I don't really see a need to do so, though it'd likely depend on who else they bring in on the villain side. If it's Alexander Lukin, then they'd probably stick with the Soviets. If they decide to tie Winter Soldier to someone else, say, Baron Zemo, then obviously it'd be HYDRA instead.
In some ways, the story already was
changed to HYDRA. It's been hinted that Bucky survived that fall into the frozen river because of the experiments Arnim Zola performed on him.