The penalty for possession of illegal fish depends on the regulatory framework under which that particular species is regulated.
For example, FW stingrays and piranha are regulated in California under the California Fish and Game Code as species that are potentially detrimental to humans or local aquatic species. The California Department of Fish and Game enforces these statutes and regulations. Because these species are regulated due to a perceived danger to humans and the environment, they are typically killed by CDFG wardens.
On the other hand, the Asian arowana is federally regulated under both CITES Appendix I and, more importantly, under the Endangered Species Act. A CITES certificate would get you past the Lacey Act, as it shows compliance with international laws, but a CITES certificate does not get you past the Endangered Species Act. Thus, it is the Endangered Species Act listing that is the legal impediment to the importation, possession, sales, etc., of Asian arowanas. The ESA is enforced by the U.S. Fish and Wildlife Service. Because Asian arowanas are regulated as an endangered species, they are not killed by USFWS enforcement officers. Rather, the care of confiscated Asian arowanas in the U.S. is typically entrusted to public aquaria, educational institutions, or even trusted private citizens with USFWS authorization.
Yet another example are those species that are federally listed as injurious under the Lacey Act. These include snakeheads and walking catfish, to list two examples. The Lacey Act injurious wildlife provisions are also enforced by the USFWS, but, unlike ESA-protected species, these species are typically destroyed when captured.
Thus, it all depends on the regulatory framework under which a particular species is listed/regulated.