Post updated with a major Punisher panel scanned from the Secret Empire: Omega comic added to it.
You can breathe easy now. Secret Empire is now officially history.
WARNING SPOILERS: Secret Empire: Omega #1 has Punisher turning against Hydra after he found out that he was being used by HydraCap to carry out his will and realizes that what he believed about what HydraCap is doing to rid the world of crime is wrong. So he threw away the HydraFrank persona and goes back to his old self again. He blares out, "Now it’s time to set things right." and starts accumulating a big Hydra body count, proving to Nick Fury that he's ready to take possession of the War Machine armor and use it which will happen later on in Marvel's Legacy series.
I honestly hated HydraFrank. I got mad when I first found out about what happened to him months ago when he first became a Hydra Agent and starts carrying out orders for HydraCap. I was like "FRANK!! HOW COULD YOU!!" The true Punisher would never even think about joining forces with the enemy whom he had battled against for many years. It was like Kobik warping Frank's reality to where we find Frank suddenly admitting to killing his own family or burning his harps. It would be a total shock if that happened. But thankfully she never did anything like that to Frank.
Frank joined Hydra free willingly because he wrongly assumes that Cap has taken over Hydra so he that can manipulate it into helping him fight against injustice and evil and has offered him to have Frank's family back alive using the cosmic cube and help him raise an army of Punishers to fight crime.
Huge mistake to which he now realizes. Frank admits that it was the worst mistake he has ever made, blindly following a "leader" who made false, empty promises that he'll never keep. Coming to his senses and seeing the error of his ways, Frank threw away his Hydra persona and instantly went back to his old self.
And now, on the road to redemption, he'll take the War Machine armor suit and use it to enhance his one man war on crime.
Welcome back, Frank. Glad to have you back.