I finally found time to do some extensive testing and unfortunately, I do not think that butchering is going to be viable. There are a lot of small bugs with it that make for a frustrating experience. First off, even without [FISHITEM], dwarves (very rarely) pull out raw fish. These items are not stored in the stockpile though and just sit under the dwarf that pulled it in. It happens very rarely and inconsistently. Dwarves will fish for months and maybe pull in one raw fish during that time. I can only assume that this comes from the [VERMIN_FISH] tag, but I am not sure. It also seems that only one live fish can be caught at a time per fishery (i.e. even with multiple "catch live" orders only one dwarf will fulfill it). This means that you have to have a fishery per "catch live" dwarf. In addition, you have to manually order "catch live" every time a fish is caught. I believe this is because the "clean fish" order (which is automatically created) overwrites it. The butcher's shop also automatically creates "butcher" orders, so getting a butcher to stop butchering all of your live fish (that aren't in an aquarium) is almost impossible.
Of note: In the first test fortress I ran today, for whatever reason the dwarves refused to do the "catch live" fish order. I am not sure why. They would not grab an animal trap and go to the river. I assume it had to do with the order I set the profession/built the trap/built the fishery/made the "catch live" order, but like I said, I don't know. So, I deleted that save and started again. In the second test fortress, I could once again visibly see fish in the water (as intended), but for whatever reason nothing was being "caught live". The dwarf trying eventually died of thirst. I ordered it again, but once again the dwarf went to the water and tried for a long time. In the third test fortress, after catching live fish for awhile I got a message saying that the area was no longer suitable to catch "live fish". During all of these tests (and the paragraph above), I made no changes to the raws.
So, I am going to add the fishitem, not_butcherable and small remains tags back. I will keep all fish cookable live and keep small fish live caught only. I am not sure what this means yet for roe, oil, etc. but I think that this is the best way to handle fish for now. butcherable vermin_fish seem to have a lot of inconsistent and non-reproducible bugs.