I think Sensei definitely planned on fucking Rin in the beginning:
Things were just complicated by Rin trying to set him up with Futaba, revealing she liked girls way more than guys, crushing on Chika, and the next Rin event after invading her privacy and seeing her topless, led to him seeing her like this:
and the one after that, has him walk in on this:
Sensei seemed unable to find an excuse to groom Rin before losing complete control over the situation. No dream for stability like Chika, no insecurities like Futaba, and no daddy/mommy issues like with Makoto and Ayane, etc. There wasn't much he could take advantage of, to make it seem like he wasn't taking advantage of Rin.
After this, he seemed too scared by Rin's unpredictability to prey upon her. This eventually led to him viewing her as something more than just a sex toy though, and even something to be treasured.
I also don't think Sensei really cared about any of the girls he's fucking, until after he already got physical with them (except Niki and maybe Ami optionally). Initially he just used them, and in most cases he's still using them. Only recently has he really begun to care about them as people. There's a reason Makoto, with tears in her eyes, had to ask him to treat her like a human being:
back in Chapter 2.
Even current Sensei who is beginning to care, is still taking advantage of the likes of Chika, who has been so fooled by him that even Ayane seems confused:
Not to mention how he literally just risked Miku's life to cover his ass.
More or less, I struggle to see Sensei prior to chapter 3 truly caring about the girls he's fucking around with, at least more so than something like "it'd suck to be unable to fuck them again". Besides Ami, optionally.