Oof she's in deep and with koichi's help she's in the best position to take down the cult and having Kamome constantly snooping and getting caught doing it is probably complicating things for her and their plan
my personal cope: They faked his death and assigned another task for him. She stabbed him to get his blood on the knife, just in case any thorough members who might "check her work" behind her and tested the blood's DNA, but replaced the body with someone else of similar build before torching it. Koichi seemed to genuinely like him so i would assume he wouldn't just allow him to be killed or they would have done it at a more convenient time (which, in the murder cult, is plentiful).
I am pretty interested to see more of Megumi's perspective now though. I wonder how long her and koichi have been in kahoots.