I have the same problem with my 2009 Honda Civic Se I-Vtec 1799cc 5dr Auto and have posted a thread with no answers to date. However looking at the rails it may be possible to put a spacer between the floor and the rear of the rail but the front would need a riser in the form of a kinked piece of metal in the shape of an 'S' with the tails cut off, that could be bolted to the floor using the existing attachment point and then bolting the rail to this item. However this may not be safe as it would not have been tested for excessive 'G' in the event of an accident.
Because of the safety implication I would suggest that the above is not a viable option and that you stick with what you have or change your Civic. Don't buy the same model as I have as it has the same problem.