From what I read, DR Jennifer, Jennifer Garner's pregnancy is NOT being written into the scenario of ALIAS. They're going to be filming this summer before she gets too far along and also plan to have her be photographed from the waist up in many shots.
To be honest, with ALIAS scheduled opposite SURVIVOR, JOEY/WILL & GRACE, SMALLVILLE, and THE O.C. next season, I don't expect it to last past January. I think ABC will cancel it midseason.