Just a clarification, I don't think this scheme actually uses deep packet inspection. Comcast contracts
MarkMonitor to monitor P2P networks for known infringing material. MarkMonitor's IP addresses are blocked by several popular P2P blocklists, including Bluetack so it's unlikeley that they'll catch many infringers except the low hanging fruit who aren't using blocklists or proxies. Another reason I don't think DPI is involved is because right after 6 strikes was implemented, I got a letter from Comcast specifically saying that they would not use deep packet inspection for this. Now I know that Comcast is slimy, but I don't think they'd reneg on such a specific customer promise so fast and voluntarily largely because of the two costs of DPI you touched on - the additional hardware/support for the program, and loss of goodwill among their customers.
Secondly, the 'pop-up' isn't actually a 'pop-up' per-se. They aren't actually interleaving javascript into your web pages to make a popup appear on a normal web page you'd browse to (how would you even do that?). Instead, they will serve a whole web page with the warning when you make an http request, which doesn't require DPI or but merely requires that they know you're visiting an http address, which they know from your port and/or url.
All in all, except for the marginal benefit to their NBC counterpart I don't see anything for comcast in this except to do the bare minimum so they can appear like they're helping to curb piracy to keep pressure off them from the government and IP lobbying groups. They know that their most active customers, the ones they can sell higher bandwidth to, are largely copyright infringers. But by doing this, they can
appear to be doing something, because there is a significant amount of infringes who are using P2P and taking zero precautions so Comcast can come back and say 'yes we caught X bad guys, we are helping'