The Ghostbloods 100% strike me as an evil organization. Not in a mustache-twirling way, but in a "trading a teenage girl to a mad scientist who will almost definitely kill her for diplomatic immunity is something that this organization is fine with" kind of way. Founding the Ghostbloods (and technically, we don't know that he did that yet, he may have joined and "taken over within a year" as Brandon said he could) is, if anything, more evidence for him being Evil.
Also, to those who say he wasn't evil in Era 1, Brandon has pretty explicitly said that in any environment outside of the Final Empire as a skaa, Kel would have been a villain, and then he showed us what that might look like with Miles.