the actual server itself probably works under emulation but the issue is then that when it ssh's in it still uses shell commands to detect the host type, which I can't so easily hack to make it look like Linux without breaking everything else.
The problem isn't in getting a random Linux binary to run. The problem is that you're running a software suite that's designed to not run on FreeBSD.
If memory serves uname(3) should return Linux when you're running a Linux binary, but then you're back to running a hostile program and working around anything that may arise once you have to break out of the Linux userland.