Sure it would alter the balance of power in the Quadrant, and you couldn't trust them to use the integration technology responsibly? I mean obviously Janeway would sell it that two sick Vidiians could 'bind" into a cohesive single life form that could live twice as long and healthily as "its" two sick forefathers... But I can see three possible supercorruptions of the process at first light...
1. The Sick Viddians start integrating with completely healthy alien kidnappees, taking their organ harvesting industry to the next level, which isn't so bad now that they Vidiians can harvest organs without murder. isn't so bad if you squint.
2. The Viddians keep integrating, doubling their life spans and health and ego until billions of Viddians have reduced into a single collective super Vidian, which has the potential to be a more gruesome plague than the Borg if it spreads just right.
3.The Vidiians use the extraction process which cured Neelix and Tuvok to make a super healthy Viddian and a super sick Vdiian, who is either disenfranchised into an even rougher subclass of citizen than previous, or they're instantly thrown into an oven... But they would have experimented with something like that already from when they murdered B'Elanna... But then there's a difference between creating two clones of you and dividing you into two halfyous... Somewhat?
Even though its a Prime Directive issue, to let these assholes die out before they take the universe down with them, might kathy have said "screw the Prime Directive" again? Because saving the Viddiands from the phage is almost as important as stopping the organ harvesting trade.