It obviously can't retrospectively change things, that would be the entire reason Greece would be taking the case. And yes, the European Union can technically breach all of the treaties that were set out in its own creation, vacate the Council of Europe, and ignore the European Court of Human Rights... but they're not going to do that for Greece because that would set up the mother of all shitstorms. It's the equivalent of the United States Federal government breaching the constitution and throwing out the Supreme Court because California went bankrupt.
The difference is that if the US Federal Government tried to do that it would be a crime and a warrant for the arrest of those behind it would be issued. Basically, US law enforcement agents would arrest the President and new elections would be called for. The ECHR does not have that type of power. If the rEU ignores the ECHR the court would lose its function but that would be about it. It would obviously cause internal problems for the rEU but not on the same level.
This is the main difference between the EU, which is a union of sovereign nations, and the US, which is a federation of states. Sovereign nations
always reserve the right to basically do whatever the hell they want, at the cost of possible diplomatic crisis, sanctions or military intervention. The ECHR and some parts of EU might have to be restructured but if all other members are in agreement it changes little.
But this is beside the point. The rEU could create some function to expel Greece legally if they wanted to. The constitution-equivalent of the EU are a set of treaties that can be renegotiated if need be.
And I should probably reiterate that I don't think any of this is particularly likely, my point is simply that just because there's no current mechanism for the expulsion of a member doesn't mean that such a thing is completely impossible.
"Remnant EU", as in the remaining members in the scenario. Shamelessly stole it from the Scotland independence debate where rUK was used a lot. I think it's rather nifty in discussions like these to quickly separate a union in its current state and a union after it hypothetically loses a member.