Indeed, the moment is a bit muddled. But, yes, the father did it. It was he (as far as we know from the episode) who stashed the case there.
The explanation is, as Morse reassures Thursday when they've examined the contents of the sample case, that the convicted Phillip Clemence was indeed the killer, as the *actual* murder weapon (a bloody hammer) found in the case definitively (though well after the fact) proved. The problem was, that *another* "murder weapon" had already sealed the fate of Stanley's father.
The crisis here is: if *that* case had been "given a nudge", what other cases over the years had been similarly nudged (even without Thursday's knowledge)? All of Thursday's (and Morse's) cases would have to be reviewed for similar improprieties. Every conviction would be called into question (among other things, putting even more pressure on Thursday as his proud career and legacy fall into disarray).