As it was already mentioned...
The distance to the Bajoran wormhole end in the GQ was practically the same as the distance between Voy's starting point and the AQ's Federation.
Technically speaking, Janeway might have known about the Dominion given the fact the ship was indeed launched months after the Odyssey was destroyed.
But, that information could have been known only by her and some of the highly ranked officials on her ship at the time (such as her first first officer - not Chakotay).
Chakotay apparently had no idea who the Dominion was. He only referred to them as 'an ally from the DQ' who supplied the Cardies with ships and weapons which lead to the extermination of the Maqui.
That only proves the Maqui had no idea about them, but not Janeway, and possibly Tuvok.
Aside from that... I would have still picked the same route as Janeway.
Given the unreliability of Wormholes, and how many times the Bajoran one was threatened with destruction/closure over a mere 7 year period, Janeway might have taken into account the possibility that this power struggle might occur at some point seeing how the Odyssey was destroyed as a mere demonstration, and chose a route that wouldn't potentially result in something like this:
"We're at the coordinates of the GQ Bajoran Wormhole".
-Looks out the viewscreen, but no wormhole appears.
"Where is it?"
"I'm detecting residual neutrinos, but nothing that would correlate with a subspace matrix of a Bajoran Wormhole. It was here at some point, but sensors indicate is was collapsed approximately 3 decades ago".
With devastated looks on their faces, Naomi Wildman (who was now in command and approximately 65 years of age) orders the conn to set course for the AQ.
Even at maximum speeds, it would still take them another 75 years to reach the Federation.
So the crew effectively doubled their journey if something happened to the Bajoran Wormhole in the time it took them to reach it.
Seriously... why would you take a route that would take as much time to get home and rely on a chance that a subspace phenomenon (controlled by aliens who are outside of space-time) would still be there by the time they reach it?