If the issue with Punk being taken out of the Scramble was a legit move made necessary by an injury of some sort, I can understand it... but for some reason, I believe it was meant solely for storyline purposes (i.e. to kick off a feud between Orton/Priceless and Punk), and pulled off in a way that should not have been.
They could at least have the attack happen at the RAW prior to the PPV, then have Adamle announce that a suitable replacement will be found for Punk at the PPV - this way they could have lowered the disappointment level if people knew beforehand Punk was cancelled (which is bad enough in and of itself, simply because he is/was the WHC and thus one of the supposed 3 top guys in the organisation - to have him NOT appear at ANY event, even more so at a PPV he is advertised for, is always a bad move), and additionally, they might've created some anticipation as to who the replacement would be by not revealing him until the match (with most people probably thinking it could be Orton, or even Cena (despite his injury - see his Rumble return, it might not have been out of the question) and the swerve with having it actally be Jericho would still have worked.
As for his win devaluating the feud with HBK... I don't really know about that. I mean, of course it makes his loss look less impactful, but then again, YJ2 sold the effects of his match with HBK apparently, and only managed to sneak a cheap win instead of really being able to make any offensive impact whatsoever; so I think it will go ok. Plus, it gives HBK a reason to still continue the feud - for if he had just destroyed Y2J now, HBK would have had his revenge, and the feud could be over. But with Y2J crawling back from his beating and becoming WHC in the process could piss HBK off to some extent, as I've pointed out in my earlier post, feeling that he "hadn't achieved enough" or "done enough damage to Y2J to make him learn his lesson", so that when he returns after his injury, he could be quite after costing YJ2 the title again, just to make his punishment complete.
Because this way, even though the heel Y2J got his ass handed to him by HBK, people will still not feel completely satisfied by it, simply because he, who should by all means have been destroyed by HBK's rage, was STILL able to come out on top in some cheap way at the end, and people might wish for HBK to once again kick his ass, and this time take the title from him too, so he has nothing left at all.
So I agree - it was a bad move to leave Punk off the card at such short notice (unless it was necessitated by a legit injury), because it definitely disappointed a lot of fans; but I think it was a good move to put the belt on Y2J, even in such a fashion, as it works for his character and could even add to keeping his rivalry with HBK alive, when by all means it should have ended when HBK handed his ass to him the way he did.