Can the university you work for or study at protect your identity by listing you under a pseudonym?
This is commonly done in several types of cases:


by women who want to retain using their maiden name professionally while switching their legal name to their husbands
by students from countries who have taken a hostile stance towards the United States and who want to protect their extended families back in their home country
By foreigners with impossibly long (from an American standpoint) first or last names or who use non-mainstream variations on their name
By faculty who go by their middle names or nicknames not their formal first names
By aforementioned stalking victims


If you are at a large enough institution, they are prepared to handle these types of situations. My (large enough) institution has the following:


Fields in the university directory database that allow for 'nicknames' to take the place of names. Because all of our e-mails are firstname.lastname@myschool.edu, this allows for e-mails to arrive properly.
Flags in the university directory that particular information should not be publicly released. One can prevent the listing altogether if you choose. 
The only other place where names would appear would be the faculty/staff/student website, which is under departmental control and easily changed.


One of the doctoral students that I work for is from one of the aforementioned hostile countries and you will not find any web presence for her on the departmental website.

This gets trickier when you are faculty, as students need to enroll in your courses and you need to publish. I would recommend in this case either a full legal name change or pushing your university/department to recognize a pseudonym. It helps greatly if you have a common last name and only need to modify your first name.