This is one aspect of that episode that I don't think was particularly well explained. I think it was injected into the script just to "swerve" the audience. However, it does seem like telling The Doctor that she was pregnant was part of the Silence's plan. The evidence of this, though, doesn't show up until the later episode "A Good Man Goes To War".
Just looking at "Impossible Astronaut", there's only two things that Amy knows that The Doctor must know but can't know: that she's pregnant, or that he's going to die at Lake Silencio.
We, the viewer, don't know anything about Amy's pregnancy until she finally tells him, so for the bulk of the episode, I think we're supposed to assume that they were talking about his death. This leads to two possibilities:
- They wanted her to tell him about Lake Silenco, and she got it wrong.
- They wanted her to tell him about her pregnancy.
Honestly, it doesn't make any sense for The Silence to want The Doctor to know either of those things. They should want Amy's condition, including her captivity, a secret or The Doctor would try to stop them. And, they shouldn't want him to know about Lake Silencio, as it would give him the chance to find a way out of it.
However, when we get to "A Good Man Goes To War", we can see that Madame Kovarian seems to have expected and planned for The Doctor to show up at Demon's Run to rescue Amy. She even planned for him to win at Demon's Run. As far as we know, her plans went off exactly as she wanted right up until "The Wedding of River Song", when The Doctor's knowledge of his own death let him figure a way out of it.
Why she would want this isn't clear, though she does gloat about it to The Doctor after pulling it off. Perhaps she genuinely thought that her army could defeat him, or perhaps she wanted him to feel despondent about losing Amy's baby, or maybe she thought it would weaken his bond with his companions.
Whatever her reasons, in the end, knowing that Amy was pregnant played right into Kovarian's plans, while knowing about his death helped him thwart those plans, so absent any better explanation, I think we have to assume the Silence meant to Amy to tell The Doctor exactly what she did.