Well I certainly think that it is strongly implied that they knew Ripley was impregnated due to the scan at the start of the film.
I tend to think that Bishop (android) had some trouble reading the data. He WAS pretty messed up.
From the film makers point of view at the time, I think they wanted to imply that the rescue team knew Ripley was impregnated from the get go given the scan we see at the start and Bishop informing Ripley that "it all goes back to the network."
The fact that they stuffed up is just that, they stuffed up.
Now for us to come up with theories as to cover their stuff ups, then I suppose your idea that they wanted her quarantined simply because of her knowledge may hold up - they wouldn't want her blabbing away to the prisoners.