That doesn't make any sense at all. Don't you mean 'if the Danes hadn't done that stupid Stockholm slaughter'?

Anyway, do take note that the Kalmerunionen wasn't ever official. So not only was Sweden not a part of Denmark, they didn't really even act as the same country...(EU III does a surprisingly decent job of simulating this, actually.)
The problem with Sweden during the Kalmar Union was that the nation was practically unfond of any ruler they got hold off. Practically every Swedish historian today considers the Swedish revolts of that age a national revolution against the evil Danish surpressors, but I have investigated the subject and my conclusion doesn't quite approve that proclamation. First off, the Swedes didn't want to be ruled by anyone. At most of the time during the 100 years age of the Union, the Swedish nobles had a habit of simply removing
any ruler from the throne. The wars in Sweden weren't only consisting of Danish Imperial Horde and Swedish Liberation Army as the Swedes might suggest today. When we Danes didn't interfere in their nation during the 20 year breaks or so that they got, they fought themselves instead. The nation was practically in civil war. Hence my comment. The Stockholm massacre was the result of the Swedes once again feeling like changing their government to the non-Danish side, and they would have been independent even if the Danes didn't interfere in it (I guess you know what it was about).
You could say that they revolted because of the Danish replacements of their nobles, but actually the Danish king removed a quite numerous number of Germans compared to the Swedes. The reason of this was to keep out German influence of Sweden, and the Swedes didn't want that either (They threw away German kings a few times if I recall).
Oh, and they were treated as being a part of a Union, actually quite like Slesvig-Holsten. Sweden was simply quite difficult to get hold of, compared to Norway fx, since Sweden was an elected monarchy just like Denmark, while Norway wasn't. The Danish king did do some activities in Sweden, but he didn't get hold of the nation long enough to maintain complete control.
... And if you'd like EU3 to be real about Sweden, make it bacon, -3 Stability and an angry vassal of Denmark (Although EU3 does start in 1492 right? If so, nevermind) without paying her master before the stability becomes positive.
My opinion at least.