That would be one of the cases where it could be reasonable (rather than just fanboyish) to use dozens of warp nacelles...
Redundancy and robustness would be necessary in every respect. In things like life support, one might devise backups to backups, all the way down to making the ship's innards big enough to actually self-support an ecosystem the same way a planetary surface does. That is, assuming that there was a reliable power source that could stand in for the sun. Computing could be backed up, too, down to the good old trick of using a thousand abaci in case everything else fails. Power systems might be redundant, with fusion and fission and perhaps chemical processes for transforming an internal type of fuel into desired energy, and with taps for harnessing the energy of cosmic rays.
But it's difficult to see any sort of a backup for the drive system. If primary warp fails, it's not as if the mission could succeed on some sort of a "secondary warp" that only gives half the speed; doubling the travel time might well mean death to all. It wouldn't be trivial to have the ship withstand six centuries of travel when she is intended to do the trip in three, I'd think.
Also, primary power for the primary drive might be a tad of a problem with 24th century tech. Antimatter fuel would only last for so long; certainly one wouldn't lightly store 100% extra fuel aboard in case the travel time gets doubled, and the ship might run into deeper trouble than that... The interstellar medium wouldn't cater for fuel replenishment, even if cosmic rays might keep low-power systems such as life support running.
But wait fifty years and the Federation might have a working system of zero-point energy taps - assuming that the noncanon idea that ZPE systems are use in the quantum torpedoes holds true. Those would then be a plausible primary power source for an intergalactic vessel. I wonder if the Kelvan device from "By Any Other Name" was of this sort?
Timo Saloniemi