I found the project http://www.cheap-thermocam.tk/ a few days ago and planning to do it.
I got an arduino uno and a MLX90614ESF-DCI coming.
Great, I've done that project too and it runs perfectly.
First thing, if you have any input on the following post, that would be very much appreciated
What's your problem with that post? The original poster there wasn't sure about libraries to be used. But this isn't a problem if you rebuild a project and use the available code.
Secondly, you are saying the configuration code (and maybe the main sketch as well) is not well written (and maybe even not working).
It's not badly written, it's just not that pretty code. But it works OK if you do the same thing as the original author. If you change a component you either should know what that means to your project or you better ask in the forum.
Would you have another code I can run ?
That's not necessary, the code runs OK on the specified hardware and the described wiring.
What is the difference between a code you can run on your due and on I could run on my uno ?
jay_ar wasn't running it on a Due but on a Leonardo. The Leonardo hasn't the hardware I2C wired to pins A4 and A5 as the UNO has, that was his error. If you're using an UNO you could follow the description on the website.