Reusing CFG structures

Ball Larus path profiling requires temporarily changing the CFG by replacing backedges (such as those caused by loops) in order to determine instrumentation placement, and attaching increments to edges [Ball96]. As far as I understand the CFG available through the BasicBlock class directly corresponds to the IR. I would rather not change the IR except to insert the profiling code. So, is there a graph structure that can be reused for such a purpose? Am I approaching this the wrong way?

Thanks

[Ball96]
T. Ball and J. R. Larus. "Efficient Path Profiling."
International Symposium on Microarchitecture, pages 46-57, 1996.
http://portal.acm.org/citation.cfm?id=243857