Definitely does add more to the no kill rule which mind you I think can be argued is more about keeping a potential villain in use.
Even if not the direction you plan to take a villain, yeah a problem for the DCAU nonetheless is the lack of restraint with the more layered villains falling into overuse without maintaining the writing that their earlier entries provided.
Freeze's only TNBA appearance in Cold Comfort avert further decline by lack of a following appearance save for his only Batman Beyond use. Keeps him from redemption, but Meltdown does him more justice that CC.
Two-Face, yeah. A Dini written story in the tie in comic does explain why Batman eventually gives up on concerns for Harvey, but you could still do a darker variant of say The Batman's episodes Clayface. Basically replace Harvey with a copycat Two-Face while he himself ends up meeting an untimely demise. Judgement Day was a nice idea, just one that should have been sooner.
Heck, I still like Dan Slott's Batman Adventures run and he did the character more justice than the latter DCAU episodes by well using the original comic trait of him occasionally doing good. Specifically is only appearance has him unable to see the result of his coin flip during an attack on Arkham and until he is able to get to it, helps Batman either the other inmates.
Or his appearance in an opening to a Batman The Brave and the Bold episode where he both fights and teams up with Batman in the same segment.
Amalgam Universe resident Born in 82.