Daas Yochid: “If they enter the fish in a krill, we have to deal with the issue of why they don’t obtain the status of the krill (as part of its flesh) and should be assur.”
The only reason they would become assur is because of “ha’yotzei min ha’tamei”, and the Chavos Daas 82:2 says this does not apply to separate bria.
“If indeed, we were to know for a fact that they are swallowed when microscopic, I could easily hear a sevoro to be matir”
I seems that the scientists believe that anisakis cannot live without a host beyond this stage of development. While they may be wrong, I don’t think that possibility creates a safek d’Oraisa.
“The gemoro, and S.A. with meforshim, clearly deal with the issue of whether the worms come “meialmo” or are “mino gavli”. A worm found in the flesh is “mino gavli”, and one in the viscera is “meialmo”. This argument, however assumes that even worms which came form the outside are mutor!”
True, however “Rav Dessler points out that the reason mentioned in the Gemara for the ruling of the Chachamim is not necessarily the only possible reason. The Chachamim gave the reason that was most obvious in their day”. Therefore it may be that the heter of the worms is not really minei gavli but because of “predation”. According to this anisakis worms found in the gut would also be mutar and this explains the words of the Beer Heitiv and Pri Megadim that even these worms are only assur mi’safek. The safek would be if they are anisakis which is mutar even in the gut or a different species which may have been swallowed free-swimming.