Homing Endonuclease seeks out certain sequences in DNA and cleaves it at that point. Normally a ligase would simply find the two cleaved ends and fuse them together with some small ATP cost. However, if the enzymatic functioning was broken, leaving one cleaved end difficult or impossible to rejoin to the other, the endonuclease could impair or kill the host cell. While typically only short sequences of base pairs are recognized (as few as 6 base pairs in restriction modification systems in bacteria), mega-endonucleases which recognized far larger sequences might be developed to operate only sequences of base pairs associated with the patient's cancer.
If perfect, only recognizing the cancerous cells, inundation of the patient with the broken homing endonuclease could be sufficient, but delivery via virus is certainly also a possibility.