This show isn't supposed to be canon, as far as I am aware. It's just one of may interpretations of this corner of the DC universe, so I don't see giving Joker an in-depth origin as being a problem, or having any impact on Batman stories past and future. As long as it's a good, entertaining story, I'm happy to see what the writers can do with him.

Fish should of of just stayed away and came back later on in the season or next season.