Ok, I managed to find this answer, which gave me some clues as to what was happening.
It appears that Chrome will not load in external resources in the extensions. Hence when I tried to load jQuery via google, it wouldn't load it, and crashed out the entire extension.
The reason I was trying to do this, was so as not to cause an issue where my multiple versions of the jquery conflicted between my extension and the target site. However, the answer indicates that the processes are essentially run in isolation, so it shouldn't have an issue. With that in mind, I've just added jquery into my extension manually and loaded it directly. this appears to work fine.
manifest.json
{
"manifest_version": 2,
"name": "Hello World",
"description": "Simple Hello World Extension",
"version": "1.0",
"content_scripts": [
{
"matches": ["http://localhost:46950/"],
"run_at": "document_end",
"js": ["jquery-2.0.3.min.js", "popup.js"]
}]
}