Pretty logical - and I'm pretty sure Mephy said he handpicked people, but I could be wrong (too lazy to check on this).
I think the other cram school students registered earlier than Rin, though; Rin came pretty close to the beginning of the new school year - I would assume the others (not including Shiemi of course) registered sooner, not to mention Mephisto was ready to kill Rin in the first place.
So, I think rather Mephisto must've known he'd need to be really picky, or, (as this now goes into a crack theory) - Toudou may have been told to get more recruitments, or more-so spies like RZ. He must've noticed the others wouldn't work like RZ, so why not do what he did with Mamushi - have them go through their training and then betray the Order later? But, the issue with this is they probably had the revival and all that other shizzly-dizzles planned out for that date, so they may have had no need for Bon and Koneko.
Anyways, Mephisto knew about Izumo, too, right? So...He purposely wanted Takara, Shura, and Izumo - and of course Rin - so that leaves Bon, Koneko, RZ, and Shiemi.
Mephisto may have realized something was going on in the Myodha sect so maybe that's why he recruited them? Maybe he found out Bon's goal and had a little laugh at that.
Shura was probably dismissed after Rin was brought out, it'd make barely any sense otherwise.
So...before Rin:
Takara, Izumo - possibly Bon, Koneko, and Rz.
So.....ya know, Takara does his thing and lets Izumo get kidnapped. Well, Takara isn't going to attend cram school. Now THAT looks bad on Mephisto - and I'm pretty sure he wants to keep the order sustained on top of it. So, that's probably why the Kyoto trio were allowed in.
Then of course came Rin and Shura.
Shiemi on the otherhand...Maybe Mephisto saw Yukio and Shiemi's potential love-life (Maybe even RinShi?) and thought it'd be a fun little game to throw in there? I'm not really sure; unless he knew she had tamer ability.
Then again, they don't have any doctors that year, Mephisto may have thought it was a good idea just for that she had the experience with the plants, even if he didn't know she was a tamer.
Sorry if this is rambled ^^;;