This also makes it very difficult to maintain for your client and a pain in the arse for any other designer or coder who has to deal with your work.
IMHO, unless your client is completely aware and onboard with this and has access to the original, un-adulterated version, you're doing a disservice to them.
(I say this as a designer and coder with degrees and 10+ years of experience to back up my opinion)
I actually encourage you to do this with the final version of a back-up copy of your homepage design. Homepages rarely change, in my experience. So, it's a good compromise. Any developer is going to work-up on the un-adulterated code, not on the obfuscated version. I am sorry for not being clear about this.
As an automated deployment step, I have a little less of an issue with it, but it's still highly dependent on the client. If they are unaware that you are doing this and do not have the ability to access the clean source files then you are depriving them of the ability to update their site. Sure, sure, nobody wants a client messing up their nicely crafted work, but in the case that you two part ways or you (or your shop, if you're not a freelancer) can't do something for one reason or another, then the product you've sold them is verging on defective unless the crippled source deployment was explicitly agreed upon.
When you do work for someone else, in most cases, the client expects (and usually contractually ensures) that they own the work you do – and it's a reasonable expectation that it'll be revisable.
In general, this just comes off as spending way too much time to prevent something that probably won't happen because rarely is your work as good as you think it is (most of us suffer from this =) and if it is good enough to want to copy, given the nature of HTML/CSS/JS, etc., if you go out of your way to obscure things too much (and if it's a trend), the motivated will find a way to undo your obfuscation in a programatic/easy fashion.
IMHO, unless your client is completely aware and onboard with this and has access to the original, un-adulterated version, you're doing a disservice to them.
(I say this as a designer and coder with degrees and 10+ years of experience to back up my opinion)