Yes. I'm no expert here, but I think the reason that low acceleration is favored is simply that it's impossible to imagine a reasonable way of fueling high accelerations.
Imagine the old Saturn V third stage. The engine that propelled the Apollo spacecraft from Earth orbit into it's path to the Moon. That engine did all of it's work in a handful of minutes. And it used up all of its fuel doing that. I think it used part of its fuel, actually, helping the craft to attain Earth orbit also. But the principle is the same; such a huge tank (larger than the spacecraft) using up it's fuel very quickly. In my post I toyed a bit with the idea of something similar burning for, say, a month. To get up to very high speed. But that was just playing with theoretical possibilities. Fueling such a thing would be practically impossible.
Ion drives and such, while very low thrust, are actually able to operate for long periods of time. Very long compared to chemical fuels. So they are our best bet by default.
But it does look as though moving at really high speeds is dangerous enough that the danger is a bigger problem than the fueling.
also bear in mind you are limited to 2 g's for manned craft (assuming you want live/living/work crew) - and not chriogenic(sp) -I'm sure there would g-limits for frozen bodies too (just have no clue what that would be), assuming you want to revive them later.