First, the USS Voyager is captured and brought into the sphere's center.
Second, the USS Voyager had limited shielding.
Third, the USS Voyager's new armor had been disengaged. (Notice the skin of the hull as the USS Voyager leaves the explosion.)
Fourth, the USS Voyager fired a new type of torpodoe that can destroy a Borg cube with one shot.

I would think with all the factors mentioned, that the USS Voyager would have been FUBAR by the explosion.

------------------
"If Morden is afraid of green penguins, and Draal is shown to have
access to them, a speculation would be that Draal will use them
against Morden in the future. However if Draal only has a purple
moose, saying that he could use it against Morden would be a story
idea."

- rastb5m FAQ