I kinda wonder if Cole's comment here wasn't meant on multiple levels:
Oh, definitely. There are parallels between the two, and obviously Cole sees that right away. He isn't lying about his identity nor was his own dark past motivated by greed, but he makes no excuses for himself. Both did wrong, both had to reinvent themselves ("make a new you"), both want and need to be better than their past.
Interesting, given he disapproves if you ally with the Wardens.
I think that's because the game seem to interpret that choice as letting the Wardens off the hook scot-free with essentially no acknowledgment of their wrongdoing from either the Inquisitor or themselves. Some of the others react similarly, especially Cassandra. My Inquisitor allied with both the Wardens and the Templars, but in my mind she did not do so without harsh words about their failures and what she expects from them from here on out. For me the choice at Adamant was not a matter of, "No hard feelings, you were duped," and more like, "Hundreds of my soldiers are dead because of you, the war still rages on, you WILL take their place in the field wherever you are not an obvious risk to us."
For Cole, there's also the matter of looking at the demons bound by the Warden mages and realizing that this could have been his fate as well ... who knows how many of these demons were innocent spirits before they were ripped from the Fade. Most mortals won't even know or care, but he does.
I think Cole is compassionate and gentle in general, but he is also capable of laying down the law if you make him more human. This is some of the banter that you can get between them if you've made Cole more human, which goes to show that he definitely won't let himself or Rainier do anything that he would consider evil/bad (and Rainier is obviously okay with that).
The same is true if he becomes more spirit-like again -- killing becomes harder on him, but he's still able and willing to draw that line. I think his harsh reaction to Blackwall in this banter, one of the few times in the game where he does get sharp with anyone, is based partly on drawing that line and partly on personal pain. Blackwall blunders into the whole still-raw wound regarding the original Cole's death by implicitly comparing himself to that templar, and it's just something our Cole can't cope with in that moment. Just as more-spirit Cole protects himself by being aware of "shackles", more-human Cole protects himself by drawing his own boundaries because his well of patience and kindness is no longer near-infinite now. It's a good sign that both aspects of him are able to protect themselves, IMO.
Plus, I have the impression that Blackwall is rather more insensitive in the human-side version of this banter. He makes it about what the templar feels, while the spirit-side banter is about what Cole himself feels. In that version, Blackwall almost seems to be begging for condemnation, whereas the human-side banter strikes me as him wanting to be reassured. Those are two very different things for "the murderer" to ask of "the victim".
How the heck did I miss seeing this the other day?!
That picture looks like some unfortunate magical accident merged Blackwall with Dorian, and neither of them knows WTF to make of this. 