Safely removing program from usr/local/bin on Mac OSX 10.6.8?
First, next time you get a Permission Denied from pip uninstall foo, try sudo pip uninstall foo rather than trying to do it manually.
But it's too late to do that now, you've already erased the files that pip needs to do the uninstall.

Also:

Up until this point, I've resisted the urge to just delete it. But I know that those folders are hidden by Apple for a reason...

Yes, they're hidden so that people who don't use command-line programs, write their own scripts, etc. will never have to see them. That isn't you. You're a power-user, and sometimes you will need to see stuff that Apple hides from novices. You already looked into /Library, so why not /usr/local?
The one thing to keep in mind is learning to distinguish stuff installed by OS X itself from stuff installed by third-party programs. Basically, anything in /System/Library or /usr is part of OS X, so you should generally not touch it or you might break the OS; anything installed in /Library or /usr/local is not part of OS X, so the worst you could do is break some program that you installed.
Also, remember that you can always back things up. Instead of deleting a file, move it to some quarantine location under your home directory. Then, it it turns out you made a mistake, just move it back.

Anyway, yes, it's safe to delete /usr/local/bin/scrapy. Of course it will break scrapy, but that's the whole point of what you're trying to do, right?
On the other hand, it's also safe to leave it there, except for the fact that if you accidentally type scrapy at a shell prompt, you'll get an error about scrapy not being able to find its modules, instead of an error about no such program existing. Well, that, and it may get in the way of you trying to re-install scrapy.

Anyway, what I'd suggest is this: pip install scrapy again. When it complains about files that it doesn't want to overwrite, those files must be from the previous installation, so delete them, and try again. Repeat until it succeeds.
If at some point it complains that you already have scrapy (which I don't think it will, given what you posted), do pip install --upgrade scrapy instead. 
If at some point it fails because it wants to update some Apple pre-installed library in /System/Library/…/lib/python, don't delete that; instead, switch to pip install --no-deps scrapy. (Combine this with the --upgrade flag if necessary.) Normally, the --no-deps option isn't very useful; all it does is get you a non-working installation. But if you're only installing to uninstall, that's not a problem. 
Anyway, once you get it installed, pip uninstall scrapy, and now you should be done, all traces gone.
So I've been having a lot of trouble lately with a messy install of Scrapy. While I was learning the command line, I ended up installing with pip and then easy_install at the same time. Idk what kinda mess that made. 
I tried the command pip uninstall scrapy, and it gave me the following error:
OSError: [Errno 13] Permission denied: '/Library/Python/2.6/site-packages/Scrapy-0.22.0-py2.6.egg/EGG-INFO/dependency_links.txt'
so, I followed the path and deleted the text file... along with anything else that said "Scrapy" within that path. There were two versions in the /site-packages/ directory. 
When I tried again with the  pip uninstall scrapy command, I was given the following error:
Cannot uninstall requirement scrapy, not installed
That felt too easy, so I went exploring through my directory hierarchy and I found the following in the usr/local/bin directory:
-rwxr-xr-x   1 greyelerson  staff       173 Jan 21 06:57 scrapy*

Up until this point, I've resisted the urge to just delete it. But I know that those folders are hidden by Apple for a reason... 
1.) Is it safe to just delete it? 
2.) Will that completely remove Scrapy, or are there more files that I need to remove as well? (I haven't found any robust documentation on how to remove Scrapy once it's installed)