I know a lot of companies do this. Heck, even ID software provided free source of their engines, but didn't give away their WADs. But is the PhP in this case of any value without the rest? Can anything be done with it?
If the PhP is of no value on its own and it specific to the CSS, JS, and images, then imo that totally would violate the spirit of GPL'ing the other. If that is the case and you want to have it be proprietary, don't provide the source/files for any of it (for the new stuff). If you want it to be GPL, then sell it, but make all of it free source, including the images, JS, and CSS. Note: I believe that Stallman's view (if you care) is that not providing images is ok if it is art and not source/required for the source, but I think that is a loophole that can be exploited, so I say make it all free.
However, if the PhP provides some value on its own and is usable (like one of ID's engines), it's all good and do what you want.
There is nothing in GPL that says that you can't get paid for it. Just because you have to provide the source for free doesn't mean people can't pay you for the work, it just means they can't pay you for the source. They could pay you for the bundle (which they could create on their own if they wanted for free, but some may not be savvy enough to do that). GPL is not anti-capitalist.