Did you ever resolve your problem? There can be any number of reasons that you could have found the Admin to become unavailable. I realize you may not now remember what step(s) you had done before it failed. But I hope that you have since solved your problem.
Bottom line answer to your question: yes, one can complete the entire lockdown guide, and not have any negative impact on the Admin (if all steps are followed correctly, and there aren't perhaps environmental challenges that may be unique to one's setup), and without negative impact to code (though obviously, if your own code did things that the lockdown guide "protects against", then you could have app problems also).
I've long suggested to people that they do only small steps at a time, and restart CF and test the Admin and their site, so that if something "breaks", you can have an idea of what you "just did" that may have caused it. I will say that whatever problem does happen, it can be resolved.
And some folks (like myself) can resolve things quickly after the fact, by getting on your server with you remotely to find and resolve the problem. So if you (or anyone reading this in the future) hits such a snag, and doesn't get a ready answer here in the forums, I list such folks at cf411.com/cfconsult.
(As for my delay in replying to this post, I had not been following this forum until today, focusing instead on the CF Admin forum. I'll be interested to see the kinds of problems that get raised here, and will be happy to help where I can.)