Fair enough IF they have that part of how to run the ship worked out.
To me, it really depends on whether they have to fully override the auto-pilot or not. Remember that the last time Destiny started to get low, it automatically found the right kind of star, dropped out, and refueled. If they had to turn the auto-pilot completely OFF, rather than just giving it new destination coordinates, then I agree that it would be a BIG problem.
Another fair point though it does raise the question of, "Just how fast is FTL?"
My memory is a little shaky, but... The Hammond (newest and bestest human ship, IIRC) could make the run from the Milky Way to Pegasus in something like four days, using a ZPM for power. There was mention in that episode of a HUGE speed/power trade-off, with the implication that getting all that extra speed (over the more leisurely three-four weeks of the older ships) cost an exorbitant amount.
So they really do move at the speed of plot... and of how urgent the need might be at a given time. Which, much like kicking in the afterburner in a modern jet, makes a lot of sense to the engineer in me.
The flip-side of that coin is that we've seen Destiny jaunt between galaxies before... but weren't given any frame of reference on how long it took other than 'about one episode'. Making it even more difficult to even come up with a good guess is the fact that in two seasons, they've covered about 1.5 galaxies (as far as the audience knows)... with lots and lots of stops.
Hand of Evil has the right of it for sure -- it's Speed of Plot for the Destiny.
I figured the point behind the attack from the others was to address replenishing the crew in a roundabout way but apparently not.
Yeah, when that arc started I figured:
1) The leader would die -- WAY too aggressive.
2) Most of the rest of her crew would (reluctantly) be integrated out of necessity on both sides.
3) We'd get several episodes complicated by the tension between the two groups.
It also would have added an interesting new faction to the mix -- Scientists/Civilians, Military, and the even more aggressive Lucian Alliance members.
Instead, a bunch of them were marrooned, the two most interesting were killed off, and only one 'face-level' SG actor remains under lock-and-key along with an unspecified number of henchmen. I really think they handled it poorly and squandered a LOT of opportunities there, especially to the potential distrust on BOTH sides with an Eli/Ginn romance.