If the head-to-head is that much in favour of S-K/F, then yeah maybe if C/J place 2nd at Nationals, it's an easier decision for the USFS. But if C/J win, there should be a skateoff with C-G/L. TBH though, I think the fairest thing is still a skate-off with the silver medalists because both C/J and C-G/L are viable options and depending on how they skate they could have actually both beaten S-K/F.
There were far greater odds of K/F winning this Nationals than losing it. Nationals is now a depleted field, and it's possible that C/J and C-G/L would've felt more pressure here had the top pair actually been competing. I don't see it telling us much about how these pairs do internationally.
K/F are undefeated against C/J and C/L. They've been the highest US finisher over and over again, and even their one lower score (their only one ever) was similar to what C-G/L scored at Skate Canada. Golden Spin was a good example of an event sometimes being flukey- which is why the Olympic team is based on showing consistent scoring/ability over a period of time rather than just one day at Nationals. K/F are the only pair that has separated themselves internationally this season with several 200+ scores (and they've demonstrated they can easily score 200+ with mistakes, so they are low-risk selection with great potential). They also have the record high score for a US pair, 212. C-G/L's best score is 10 points lower (and that was way above anything else they've scored, whereas K/F have had a more consistent output). C/J have never broken 200.
You sound like you'd want everything to be based on Nationals (and an unlucky positive test). Everyone's entitled to an opinion of course. But if you read the US's long Selection Procedure document, it's not like that at all. International competition matters. And the skaters have known for a long time what the Selection Procedures are and what they would need to do to get into a high Priority Grouping. And K/F did that.