I'm no rocket scientist, but wouldn't anything other than the shortest distance from A to B make for a much longer flight time?
I would think you could merely have the booster turn on and off --- still keeping a "straight" line, but changing the predicted arc from what was predicted early on (which admittedly would be longer than doing it right the first time) (looks like it would hit Chicago, but goes for Houston).
OR, have the re-entry warhead come down at a steeper-than-free-fall angle by the reverse --- e.g., a missle looking like it would hit Houston, hit Chicago (comes over the NP).