Yes, this is the perplexing bit. Even if we assume that the motive was something CV found in her diary, as you've shown, he scarcely had time to read through it.
Now killers do kill off the cuff. The Yorkshire Ripper killed a woman on his way home once, because he saw her going into a park and figured that he could. So he parked, followed her, killed her, got back in his car, drove home and went on with his evening. It does happen. In this case it requires that CV somehow recognised the potential offered by SJL's rearranged visit, did her this harm, and hid her, all within his first hour in charge of the pub. He did this knowing that if she were ever found there, he would inevitably be incriminated.
We have no way of knowing if he'd ever set lustful eyes on her before she turned up, but I'd guess not. He was only the temporary guy, he'd only arrived that weekend, he had trained there in the previous six months but there's nothing to suggest he'd seen her in there before.
The police are still wrong to insist that they can't think of a motive, so it can't have been anyone at the pub, so let's not bother searching it. Just as a matter of procedure, it's an obvious omission not to identify all the places SJL may have gone, to note that the PoW was one unaccountably never searched, and to rectify that now. CV's story change to include phone calls and the total failure to mention anything to the permanent landlord both seem quite fishy to me.
The problem is that the police are fixed in the mindset that there would have had to be something "salacious" in the diary to prompt some sort of attack. That's the only motive they can think of. It seems equally plausible to me that what interested CV was the mention of bonuses. What if the diary said what bonuses were due, or what swanky places she had been, leading CV to think SJL was rich? That he could demand a reward for giving this diary back?
The speed and completeness of SJL's disappearance suggest either outrageous luck, or some premeditation. This is I guess an unstated assumption behind the Mr Kipper blind alley.