Every physician practice should get an employee to fill out the FMLA forms before she leavers for maternity leave. They are available for download at: http://www.dol.gov/esa/regs/compliance/whd/fmla/wh380.pdf These are the forms that the department of labor provides. The employee’s physician fills it out and it specifically states when the patient (i.e. employee) will be able to return to their job. You should require this form for all FMLA leaves.
FMLA requires that you provide a job, not necessarily her job. Another note, if the employee is out for longer than a total of 90 days, you do not even need to retain a job at all. If she went out early on maternity leave and wants to take 3 months after the baby is born, FMLA no longer applys. I know it sounds kind of heartless, but I know in some big corporations this has been used to get rid of problem employees who were out for longer than 3 months with a pregnancy. Because it goes beyond the 90 days that FMLA mandates, it is not considered discrimination and the employee cannot sue for wrongful termination.
I think you really have to fall back on any documention you have as well as your policy and procedure manuals. When it comes to maternity leave (and really in all other situations), you should not let an employee dictate her work schedule / raise / etc. or that will set an ugly precedent in the office.