The article still produces an ELF object as its result, you need to decompose the ELF object itself to get the LLVMIR. If you use readelf on the attached file, then you see that llvmir starts at offset 0xc8 and is 0x5bc bytes in size. So, your best bet is to write a program that takes in an elf file and offset and a size and strips that section and stores it into a seperate file.
Another thing you can do is use a binary editor and remove the first 0xc8 bytes and everything after byte 0xc8 + 0x5bc.
I could extract only the contents of a section using the offset and the size info from readelf.