Well, you could make symlinks in /usr/include to the IPsec kernel headers, but having kernel headers in /usr/include for user programs isn't advocated or promoted and definitely discouraged.
I would suggest dealing with this in the makefile and have a macro for the kernel release so your gcc flag reads something like:
CFLAGS=-I/usr/src/kernels/$(KERNELVERSION).EL-i686/include
Then set KERNELVERSION to 2.6.9-11 or 2.6.9-5 in the makefile. Or you could do it through the environment, like this:
$ KERLNELVERSION=2.6.9-11 make blah
You get the idea.
Peace...
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