To solve this problem, I simply compiled with a older kernel-headers already installed on the machine (2.6.18-53.1.13.el5). To do this:
./configure --with-kernel=kernel-dir && make
The kernel module is in the directory kernel/. Modprobe will not work, instead use insmod.
cd kernel
insmod fuse.ko
This way is probably not the best way to do something like this, but it works.
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