If the rule states that a fish cannot be used as bait, and it doesn't specify dead or alive, you would best to presume that it means BOTH WAYS.
Figure that they don't want you to kill small perch (as you would a shiner) so using it as chunk bait means that you caught it for bait.
Doesn't matter if it was gut hooked and died after being caught. How do you prove that, and if it is hooked as bait it shows your intent, so that would be wrong again.
Better safe than sorry.