It's not as though he's being tried or punished for a newly created crime -- it's just a new descriptor for what he is.
From the article:
Sexual predators must register with the state for the rest of their lives...
So, basically, what this is saying is that the new law will require him to perform certain actions based on his convictions (in this case for the rest of his life). That's the definition of "punishment." If today the legislature decided that a $500 fine should go with each speeding violation, could they then make you pay it for a speeding ticket you got in 1994? Of course not, because they are adding an additional punishment based on your previous conviction. Likewise, requiring him to register with the state (for which he can be jailed if he does not comply) is a new punishment.
No one is defending child molesters here (there'd be a lot fewer problems like this if we'd just lock them up permanently... or worse), but the SCOFLA is correct on this one...