Given the principles and types of behaviors Humans in the 24th century are supposed to exhibit... Janeway was definitely in the right.
Seven of nine hesitated and had she actually opened that rift when she was asked to, there might have been something akin to several 8472 bioships coming through and destroying (or at least fending off) those Hirogen ships.
The wounded 8472 on Voyager would have gotten a pretty good idea on what the Federation is about from Tuvok given the telepathic link, which he could have shared with other 8472's.
At the very least, it could have secured a temporary truce in the case of Voyager and leave an opening that once the Federation advances more, they could potentially revisit 8472.
One thing that strikes me as odd is that how the heck couldn't have the crew of voyager done it without Seven?
They had detailed info about Seven opening a rift the second time around (when they were in Fluidic space).
And I fairly doubt that since that time no one would have taken the time to analyze the readings or that the computer couldn't have reproduced the procedure entirely on it's own (it would know the modifications were made and in what arrangements, and besides most Borg modifications were initially left intact, sans the ones that later gave issues with the Warp drive).