The avenger is capable of maintaining extreme speeds (mach ~26 is it?) while inside an atmosphere, and it does this using drive technology designed for long-distance space travel. Furthermore, neither the avenger nor any UFOs are built in a way resembling aerodynamics. As near as I can tell the attitude is "Turbulence? Hit the elerium and push through it!"
I'm fairly sure the Avenger travels in low orbit, where the atmosphere is very thin. Even if pushing through stratosphere would be possible at Mach 26, it would be horribly ineffective.
Alternatively the avengers pilot might limit herself to something like 200g acceleration or less to avoid liquifying organic tissues, like your meat-bag crew.
Wait, what do you mean 200 g? I don't know what technology you assume, but I don't think even your anti-acceleration chambers filled with miracle fluids would allow a human to survive more that 40 g. With no special equipment, a person loses consciousness after a few seconds of 6 g, you know (it's not precise data, but something along these magnitudes). And something like 40 g with no special sci-fi equipment would instantly kill anyone.
Assuming somebody thought to bring crackers and a water bottle, you could always just take an extra day or two. Of course maybe all that anti-grav tech can actually reduce the Gs felt by your passengers.
And here's your solution! Yes, internal gravity wave emitters would secure both the crew and the equipment against acceleration. Of course, if it's powerful enough.