I get the impression that Sam's hands-off when it comes to how John runs his team, and that she's still Earth-oriented enough that it doesn't occur to her a pregnant woman should have a voice in whether or not she's removed from active duty.

(And I can totally see John's point, but he really shouldn't have made it in the way that he did. Also, just telling Sam like that, "Oh, by the way, Teyla's PREGNANT" was so... oh my God, John, there are times when the pouting six-year-old is not cute. This is one of them.)