There is no "perfect" solution to this.
There is no perfect solution perhaps; but I think we can agree that allowing a website to be shut down even for an unsubstantiated allegation of copyright infringement is such a bad solution that it is worse than the disease. As written, SOPA and PIPA place the burden of copyright enforcement on the website owners and ISPs. If they receive a complaint, they have almost no way to evaluate the merit of it; but they will bear the brunt of penalties for not deleting it if it is an infringement - the default setting in that environment is that any speech that receives a complaint will get deleted in order to protect the website owner/ISP.
That is a system that cannot coexist with free speech.