I’ve always read this early moment of hers a little differently. Nodoka does care about a selected few (hence Otoha’s rescue mission and Futaba overall), but I didn’t think this moment was one of her rare caring side’s manifestations.
From what I am seeing, as a known extreme pervert and a smut novel writer, Nodoka was “excited” about finally having a chance to dig into the mind of essentially an irl harem protagonist. She will press difficult questions at the cost of making everyone uncomfortable so that she can dig as deep as she can. As in, her intend there felt like “simply learning” instead of “preventing potential harm”. Grilling him in front of audiences might help expose his true color more; or it might be an effective way to gauge how willing/honest/forthright Sensei might be when it comes to questions that directly related to his very obvious ulterior motives. No matter what the case was, I doubt the sole or the main purpose of that moment was to gatekeep (not to mention the lack of concern or questioning of the same topic thrown directly at the prospective recipients of the said potential harm if she was really mindful about this).
In other words, I don’t think Nodoka would do anything even if Sensei’s answer to the question “the likelihood of him accidentally harming any of us beautiful girls” was bluntly VERY LIKELY. Since she didn’t actively do more about anything at any other given time, and since it is so painfully obvious that Sensei WILL not hesitate to fuck everyone and WILL unavoidably break everyone’s heart, I am going to assume that her reasoning of that grill session wasn’t to protect, but to merely learn about someone that might soon become the most interesting addition to her life, in ways only she can appreciate (and I guess us too if we are still playing).
I'm not so sure that she'd stop him even then. If she figures out, or has figured out, that everyone 'resets' at a specific time, then it wouldn't surprise me to see her rationalize it out that even if Sensei were to break a girl's heart, as long as it's not one of the girls in the 'reset harem' (tm) that currently surrounds him... then there's really no harm in it. After all, when the reset finally happens, those girls who had broken hearts aren't going to remember what happened to them in the first place.
What we're seeing is a longer version of the "Groundhog Day Loop" trope, which has become somewhat popular as a writing tool for developers. On the surface, it lets you play around with different ideas or situations, with the knowledge that at some point everything will be reset back to the starting point, and by and large, whatever happened during that loop has no bearing on the future. Because, honestly, it never happened. Throwing in the idea that others can be trapped in (and aware of) the loop is a bit of a twist, but it doesn't change the fact that that's what we're seeing here.
It wouldn't at all surprise me for Nodoka to be somewhat self-aware of this trope, and fall into its typical cycle some, before quickly moving on to the second phase of that trope.
The phases, for those curious are:
1.) The character starts experimenting, then playing around with the people around them, confessing or acting on their feelings for another character, telling off their boss, getting themselves killed in interesting ways, and other things, in a form of Save Scumming.
2.)The character finally gets down to the business of what's causing the loop, and finds out how to stop it, often using the information learned in all the previous iterations to make sure this one last loop goes perfectly.
Given what we know about Nodoka, it's naturally plausible that she may skip step one like the other girls in the 'reset harem' (tm) have done thus far... but there's no guarantee such will be the case. From a writer standpoint, I'm not so sure I want her to skip that step myself. It actually could be interesting to see her playing around with other characters not directly included in the 'reset harem' (tm), to see what she could get away with, or what would happen. Which, could lead to a rather interesting dynamic should any of her playthings end up becoming part of the 'reset harem' (tm) while she's toying with them.