It depends on a couple of things: (a) how the culture treats magicians, and (b) how it treats women.
Progressive corps (Horizon, NeoNET, Evo) would probably encourage a pregnant magician to accept light duty in the second trimester, medical leave for the third trimester, and maternity leave for the first six months after birth (paternity leave, too, for that matter). They would probably provide free daycare if not a dedicated nanny or au pair when the magician is ready to resume her duties. Progressive corps figure a happy, satisfied magician is a loyal, hardworking magician.
Socially conservative corps (most Japanacorps) might discourage magicians from becoming pregnant in subtle ways ... half-pay on medical or maternity leave, delayed promotion schedules, payroll deductions for corp-approved childcare, reassignment to lower-priority projects. Magicians are valuable resources; conservative corps would prefer they focus their attention on more important things than family or personal lives (i.e., the corp).
Most corporations (and all mega corps) are savvy enough to value magicians, but there are enough anti-Awakened cultures out there that being pregnant and a magician could make you the focus of all sorts of unwanted attention. Good targets for extraction, these.
EDIT: See the "Pregnant" quality in Bullets and Bandages (p.12).