I've fallen behind a little on this thread, but from what I remember of Ms. Williams' comments at LIRR committee meetings over the past few years, she would commonly offer two primary reasons for why they are reconfiguring Jamaica as they are:
First, they no longer want to hold timed connections at Jamaica anymore. While trains being held for connections wouldn't be a significant or frequent problem if trains ran on-time more often than not, holding trains for connections does cause congestion and delays, so they no longer wish to do that. And this is not only for the Brooklyn trains, this is for all trains. So while Jamaica will still be open for business and a station where people can board and alight, there won't be any timed or coordinated connections, so you might have a bit of a longer wait or your connection might involve one or more flights of stairs over to a different platform. It would be a lot like transferring between trains at Woodside--yeah, both Main Line and Port Washington Branch trains stop in the same place, but there's not much effort made to make the train times line up, and if you want to go between them you either have to take an earlier train or hope that your first train arrives on-time, because the second one won't be there waiting.
If they continue on with having no timed transfers, it will be interesting to see how they approach it from a passenger information point of view. Will the timetables show no connection information at all, or will they do things like NJTransit does at Secaucus where they'll give you a sample connection that will give you 8-12 minutes of time to make the connection, but the trains won't hold if their connection is late.
Additionally, if the railroad isn't going to be offering timed transfers, they will have to find some way to provide adequate service to both Manhattan terminals (if Brooklyn is going to be out of the picture). There has been speculation that this is what they are planning on doing, but there's some questions on how they would actually implementing this without either doubling the amount of trains that they are going to operate (during the off-peak times, at least), or essentially halving the amount of trains that go any one terminal. For example, what would they do with the Far Rockaway Branch, which now has hourly service to Brooklyn during the off-peak periods. Would they run service every half hour now, with one train to New York Penn and the other to Grand Central (remember, they don't want timed transfers anymore, so it's not like they could run one to Grand Central and offer people the opportunity to transfer to New York Penn), or do they run trains that depart in even hours go to New York Penn and trains that depart in odd hours go to Grand Central? The former involves a substantial increase in the number of trains they are operating, the latter is effectively taking hourly service for those people who want to go to New York Penn and cutting it in half. The former is expensive, but the latter can be dangerous--if someone picks up the timetable and sees that there's only trains every two hours, that's likely the time where they'll say "screw it" and get in their cars and drive. (the LIRR's market, especially in the off-peak periods, can be surprisingly elastic).
The second reason commonly cited is a consequence of the first: with trains having dedicated connections, there are some significant ridership disparities on some trains west and east of Jamaica. A westbound Ronkonkoma train heading to Brooklyn might arrive at Jamaica, and since most people want to go to New York Penn, 1,000 passengers get up, cross the platform, and flood a tiny West Hempstead train sitting on the opposite side of the platform. Because the West Hempstead train doesn't have that many riders east of Jamaica, there's a substantial difference between the number of people on that train when it arrives Jamaica and when it leaves. As a result, the train west of Jamaica has either lots of standees and is above service standards, or they make the train longer and east of Jamaica the train is twice the size it needs to be, which is inefficient, and in some cases, not possible due to various restraints. Not having timed transfers would effectively eliminate or significantly reduce this problem, since people would either not transfer at all, or disburse on their own amongst the remaining trains.
At any rate, not continuing through service to Brooklyn is a dangerous line to toe, considering how much that area is growing and how much people dislike transferring.