Uh, for the speedreading dumbasses,
IIno was clearly goaded into this whole "make Ishigami work for me" thing by Onodera. She even lays it on Iino by implying that Ishigami is suffering from guilt unless Iino does something to help alleviate it. So no, she's not randomly taking advantage of him.
Also, it's painfully clear that Ishigami really doesn't give a shit about her ordering him around. Hell, to some degree, he even feels more validated now that he's able to protect Miko again, rather than the other way around.