This isn't the first time affiliates pre-empted ABC Programming. NYPD Blue was not carried in many markets because some affiliates found the content to be objectionable. Perhaps carriage agreements no longer allow this, I don't know, but the circumstance is similar.
You answered your own question. The NYPD Blue situation was way back in
1993. 32 years is an eternity in the broadcast industry, and therefore has absolutely zero standing as a precedent for the present.
Therefore, your second sentence is correct. Network affiliation contracts, as was pointed out in the original thread about the Kimmel suspension, now only allow for pre-emptions in limited frequency, and then usually restricted to things like expanded news coverage in a disaster or live sports coverage (since many affiliates also have contracts to broadcast their local team's games).
I would not be surprised, actually, if what happened back in '93 wasn't the spark for the tightening of restrictions on pre-emptions. Realistically, any such pre-emption creates a legal problem for the network, which sells the in-program advertising based on the presumption that the programming is being carried across the entire network. Sinclair and Nexstar are lucky that ABC did not sue them for breach of contract.
The bottom line here (as I have said a couple of times previously, in both threads): It is not the local affiliates' right to decide for their viewers what they can and cannot watch; the prevailing POV is that any "offended" viewer has plenty of options themselves if a particular program offends them. And in this case, the potential for such offense was very limited; the late night audience is much smaller than prime time viewing, Kimmel's regular audience did not take his off-handed remark to mean what Sinclair and Nexstar interpreted it to mean, his remark was not out of character for Kimmel, and outside of the misinterpretation it was harmless.
I am a regular Kimmel viewer. I saw and heard the remark. In context, it did not even come close to what the offended station owner groups claimed it was. They blew it entirely out of proportion and if anything, have likely forced the networks to tighten the pre-emption clause in their affiliation agreements even further.
Put simply, this backfired on Sinclair and Nexstar and all ABC affiliates will be further restricted as a result. (As will the affiliates of CBS, NBC, Fox and The CW, since they will likely take similar action in their affiliate contracts as a result of this.)