OP- Calling into working for several weeks is excessive. Especially considering you are probably safer there than going to the grocery store, movies, restaurant, OB appointments, etc. Also, flu season can last all the way through April. So unless you have an extremely understanding boss, I think calling in for almost 4 months would be a pretty good way to get fired. You would also have to apply for FMLA for an extended amount of time off and that would cut into your maternity leave (that's assuming your company has more than 50 employees and has FMLA).
Just get your flu shot- it takes about 2 weeks to build up a decent immunity. Go this weekend to a pharmacy and get it. Today, Boston declared a Flu emergency and nationwide, the flu is the worst they've seen. The vaccine has so far been 75 percent effective, so for me, the benefit highly outweighs any risk (which in my opinion is quite minimal). I had the Flu shot at 6 weeks when I was pregnant with DD and every year since (including this year), never had any problems.