Ok, so I'm moving my research out of my question and placing it in an answer, but I think it's now pretty clear what's going on (even if it isn't totally explicit in the movie).
Yes it's true that some of Indy's female students are obsessed with him, but the joke here is that, while he's an accomplished "adventurer", he's not so good at being a professor.
His secretary, Irene, says:
Dr. Jones, I'm so glad you're back. Your mail is on your desk. Here are your phone messages. This is your appointment schedule. And these term papers still haven't been graded.
I looked at the script, by Jeffrey Boam, and I discovered the following:
Students once again CLAMOR for his attention: "Doctor
Jones!" "Wait, Doctor Jones!" "My grade!" "My term paper!"
It's clear that Indy sees his job as a bit of a chore, and so actively avoids grading his students' work, or giving them the feedback they need. It seems he'd rather be adventuring and so neglects his duties as a member of staff at the college.
Instead of dealing with his irate students, he makes up a ridiculous scheme (whereby Irene has to try and decide who should be seen first) and then jumps out his office window.