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Your options are limited.
You can either use C++11 to extend the current TimeSynchronizer. By using cpp macros properly, you can make this mechanism totally optional which would allow to achieve your goal without imposing C++11 to the whole ROS community. It would be a reasonable design choice IMHO.
Another possibility is writing a TimeSynchronizer for several instance of one type. It is possible to do so without relying on metaprogramming. In your case, it would be sufficient.
Both would be interesting addition to message_filters, I think. But you'll probably need to fork the class you use by copying them into your own project as long as they are not integrated and part of the official release.
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