There's only two routes to getting this undone. One is a constitutional amendment, the other is for the Court to get several justices who are eager to overturn this decision, and then bring a case to trial specifically to address this issue.
I can't think of an amendment that would likely have a broader appeal than one that says presidents aren't kings and aren't above the law. But even so, I can't see it getting passed any time soon, given the overwhelming bipartisan support it would need. Personally, I'd like to see this done anyway, if only so that we could also include a provision stating that a president can't pardon himself, and can't pardon crimes that he ordered.
By comparison, it seems a lot easier to change the balance on the court, since one way or another it will be changed over time. And assuming we reach a point where we can be confident that the majority is ready to completely erase this ruling, then you just need to bring a case against a former president.
One could wait for such a case to arise organically, but that's leaving a lot to chance. You need a former president to have allegedly committed a crime, you need a evidence enough to bring a case, you need to go through the appeals process, they need to try to use presidential immunity, and then it needs to be taken up by the Supreme Court. Any number of things could go wrong, and there could be political fallout. If there's a serious enough situation that requires this, by all means, go after them and make this an issue in the case so that it has to get appealed. Worst case scenario, they get away with something they would have gotten away with anyway.
Personally, if I were president and had shifted the balance of the court back to one that respects the rule of law, I'd probably tell the justice department to bring a case against me, appeal to the Supreme Court, ask that they expedite the appeal, and then they can completely reverse this insane precedent. It would all be contrived, but that's hardly anything new. I would make sure that anyone I appointed to the Court was down with a plan like this, If they won't do that much to safeguard the country, the constitution, and rule of law, they can't be trusted with the responsibility of being on the Supreme Court.