The witch craze started centuries after the Black Death. This alone should tell you that this claim is dubious. In addition, the Black Death started in the 14th century, not the 12th, so there was no direct causal link (if the cat massacre had happened)

Actually, some days ago an Australian historian has released a blog-post about just this very misconception.

To sumarize:

• The timing is off (see above)

• The Black Death occurred in non-Christian/non-European regions as well (yes, there is a world outside of Europe), there, too, it caused massive destruction.

• There is no evidence of a cat-genocide. Quite to the contrary, our feline friends were well loved in the Middle Ages and were sometimes kept as pets by nuns. From my personal opinion: Given that cats are beloved pets and useful as mice-killers, it is very likely that a command to kill them (if it had existed) would just be straight out ignored. And the Medieval Church was not a totalitarian instution (nobody had such powers during the Middle Ages) and would not/could not enforce strict dogmatic discipline among commoners.

• Gregory IX did indeed mention cats as part of a "Luziferian" ritual in papal bull, but that statement was not generalized to all cats. And again, there is no evidence for a massacre.

• There were some instances of people killing cats during the Black Death, but people killed other animals as well (e.g. dogs), as they thought they might spread the "miasma" that caused the plague.

Edits: Minor clarifications right after posting.