During TFA pre-production before the script was done, he came back several times to the storygroup and they kept reducing Luke's scenes and Kari Hart wouldn't say exactly what they wanted.
You're right in so far as they weren't given any notes about tossing Luke aside explicitly, there was no "Take Luke down a notch" feedback or anything like that.. So yes, JJ did have to do it on his own. It was more of a silent process. Like "ahhhhh....hmmm" handed back a script with scenes crossed out but without any notes. JJ would be like hmmmm OK. It was very try-again, as far as the script writing process went.
JJ and Kasdan weren't going to keep turning scripts in to have them rejected. They had already made at least 3-4 trips and some of the storygroup visits were heated enough for JJ to swear off any more storygroup ever again, which is why he dealt directly with Iger in Episode 9 production. At the end of the day, these are Hollywood professionals. They get paid to do a job.
Once they completely eliminated Luke from the story, Kari Hart and the storygroup greenlit the script.