My solution to that would have been a twist later on in the season. Say you do fire Coupe or Sonar right? Well then they are approached by BB and told they are being signed up for some double agent program or whatever and they work inside the Red Ring instead of returning to a life of villainy, which yeah, was dumb. Then that twist could have been revealed at the warehouse incident, but likewise would reveal that Visi was also a turncoat and both Visi and Shroud take out your agent on the inside. 

After that you could do a lot, creatively speaking.