Legally, I'm not sure how it stands as regards the clubs only actually stated they intended to join a Super League - so whether bans / points deduction would be enforceable or whether they could appeal I'm not sure. But, unless the punishments were huge, I imagine all the teams would accept them and not do further PR damage with legal appeals, etc.
Whatever the punishments, they really should be for next season while it's so late in the season.
Any exclusion from Europe shouldn't be for this seasons SF's and final. But I'd accept any of the 12 being banned for next year (although Arsenal's may have to be carried over if they miss out).
And any points deduction in the league should be at the start of next season, so all clubs know where they stand when the season starts rather than have a very late points deductions skewing the table.
Personally, I think it's unfair that the players, managers and fans will suffer with either of those punishments - when they were all innocent. But I guess that often happens with things like match fixing, third party ownership, ffp, etc, when it's also the owners, not the players or fans, doing wrong.