Considering they prepared ransom to take over her spot if negations failed... Her salary might have gone down?

I think they were probably using that as insurance against her demands getting out of control. Looks like they reached an agreeable figure for all parties.
You'd also have to figure that they wouldn't have wanted to replace Mulgrew unless they really, really had to. To many she was one of the most watchable things about the show. Given its ratings woes, I doubt they'd have risked losing her to be honest.
Back on topic: every problem with Voyager can basically be traced right back to Berman and Braga.
Don't know about every problem. Didn't they both want the season-long 'Year of Hell'? Thought it was Jeri Taylor who shouted that one down.