Wow that is an expensive diode. You don't need a fast switching one.
I would say yes a diode drop in the USB line is going to give you trouble some where down the line.
The point is that you are trying to protect your Mac from something you don't know, and it looks like we will never find out. Therefore it is impossible to give any measures that will protect it.
I have used a MacBook pro for over 5 years on many different makes of arduino and have not encountered any problem. And I think that goes for every other member on this forum. So I would advise against doing this modification to your cable.
I know I am being a bit irrational about this whole thing but I can't seem to shake off this feeling that I need to secure my macbooks safety for some reason. Thanks anyways, now at least I know using a diode is somewhat out of the question. If anything, I have bought a wall plug powered usb hub just in case. (though I do feel like adding 230v to it seems even more dangerous)
I made an edit to my previous post but I will add that question to this post:
Also I was thinking would it be possible to have something like a seperate breadboard or something with a switch on it, turning the arduino on or off, but still alowing the user to upload code to it while it's "off". In that case I would be able to unplug it, hook it up to a battery and turn it on, hence removing any possible harm to the computer.