I noticed the same dramatic drop immediately after the IMA system was reprogrammed. A bulletin for this was issued in August of 2010. The IMA system had to be changed because the hybrid batteries were dying prematurely, which would have resulted in Honda having to replace them under warranty.
Following the update, I noticed that the IMA does not kick is when it used to. If the battery meter is at half or less, the IMA does not kick in at all. Honda told me I should only see a difference when idling at a stop.
The battery is not being utilized in order to save life, which results in an increased fuel cost for the consumer, which I feel is not fair.
Anyone who has this problem should report it to their dealer and Honda customer service. I have yet to get the impression that Honda is willing to do anything about it. I have also reported this to the Better Business Bureau Auto Line and my state Attorney General consumer complaint line.
If enough people complain, they will have to do something about it. My dealer said that they have had many complaints.
I suspect part of the fuel consumption increase is just winter driving conditions. Some may well be as you suspect. However I would want them to do what is necessary to extend the battery life. In the long run I suspect you will come out ahead.
I don't find this all that disturbing. New technology can be expected to have some unforeseen problems. It is part of being on the cutting edge.
That said, I would suggest doing some on-line searching now and in the future to see what might be happening. If you are right about it, I would expect a class action suite may well be on it's way.
I would wait for the class action suite. I might want to send a certified letter to Toyota stating your concern, just to get on the record if nothing else.How would writing Toyota help, Joseph? 
WOW…
According to this LA Times article, more than 4% of all 2006-2008 Civic Hybrids in California have had their battery replaced. That exceeds the threshold needed to get a solid black reliability rating in Consumer Reports (which, strangely enough, the car does not have). That also doesn’t cover the complaints like the OP about gas mileage dropping. The article talks about 20%+ drops in mileage - from 45 to 33 mpg, for instance, for one driver (33 is barely over the mpg of the standard Civic).
It also states that a lawsuit against Honda was opened in 2007, and they’re seeking class action status for it now…
Question for the legal minds out there:
Assuming (and I don’t know this for sure) that Honda knowingly re-programmed the IMA to “spare” the battery, at the cost of mileage…
This would increase CO2 output of said cars, and proportionally increase the amount of “bad stuff” (CO, NOx, HCs) the Honda Civic Hybrid puts out. Doesn’t this mean Honda would be guilty of “tampering” with EPA emissions, in much the same way that somebody who bypasses a cat, etc, would be?
Yes, it would increase the output of all emissions from the vehicle.
However, the vehicle is subject only to the legal limits for emissions that all other vehicles have. If it drops from 45 to 33 mpg, it is still entirely possible to meet PZEV emissions standards (Ford got the Focus to this standard in some states). If it still meets that standard for emissions, there isn’t a problem as far as EPA regulations are concerned. The legal issue is in false advertising and falsely representing the mileage.