SOPA and PIPA are intended to address issues with foreign-hosted sites being used by Americans to pirate American copyrighted works. MegaUpload is a domestic outfit, so they fall under existing copyright law, including DMCA.
The issue with fighting foreign-based sites is that they don't fall under US jurisdiction. Up till now, the RIAA and MPAA have taken to suing Americans using those services. However, that's not really putting a dent in piracy. So, they came up with SOPA and PIPA. Of course, how do you stop Americans from visiting foreign sites which you have no jurisdiction over? Using DNS filtering is the answer they came up with. Of course, they left the language fairly broad, and now they've stricken that part from the bill.
The real issue with SOPA and PIPA is the removal of due process. Since the laws deal with foreign entities, though, the waters get muddied.
Whether or not megaupload is guilty, it seems to me this was followed and bridged international boundaries nicking a "foreign" and "rogue site".
As an aside, I don't think megaupload fits a domestic definition. All indicted are apparently not Americans and it is a Hong Kong and New Zealand based organization.
Megaupload Limited P.O. Box No. 28410 Gloucester Road Post Office Hong Kong
Also there were pretty high profile domain seizures done in two bouts over the last two years. ICE/DOJ seized domains (google it) - some of those were foreign based but with .com or .net. (I don't recall if any were foreign TLDs) There already doing anything they want anyway - and happily ignoring any due process - codifying these actions into law with PIPA/SOPA is just the icing on the cake.