Under FMLA you can elect to use paid time off during your FMLA-protected leave. Employers often require you to use paid time off (either sick time or vacation time) to reduce the overall amount of time you are out of the office so you are not taking FMLA plus vacation in the same year. I can't say I've ever even heard of an employer refusing to let you use both.
You may have issues with both FMLA and pregnancy discrimination under the Pregnancy Discrimination Act (PDA)/Title VII. You should speak with a local employment lawyer about your options.