Janeway was fine with the Kazon taking the array initially, even though she knew exactly who they were and how they behaved. it seemed as though that she didn't believe that she or her crew were at all involved in what was happening here in the Delta Quadrant.
JABIN [on viewscreen]: Have you come to investigate the entity's strange behaviour too, Captain?
JANEWAY: All we care about is getting home, Jabin. We're about to transport over to the Array to see if we can arrange it.
JABIN [on viewscreen]: I'm afraid I can not permit that.
JANEWAY: We have no dispute with you.
JABIN [on viewscreen]: I have a dispute with anyone who would challenge us.
JANEWAY: This is ridiculous. We have no intention of challenging you.
JABIN [on viewscreen]: And I have no intention of letting anyone with your technological knowledge board the Array.
JANEWAY: Jabin, can we discuss this like two civilised
TUVOK: They're powering up their weapons.
If Jabin had not picked a fight, Janeway would have turned off the self destruct, used the array to get home and then, maybe she would have sabotaged the frakk, and maybe she would have left it intact, it all depends on after Caretaker died who was laying claim to that piece of real estate... once it was their array, she couldn't blow it up legally, and lets face it she was proposing a joint mission before everything went to hell after she called Jabin "uncivilized" and them is fighting words on most worlds, and it's like Kathryn had never had a conversation with a Klingon or a Cardassian before, to anticipate how a warlord from a savage childrace might take offense to be called names.