I don't think he'd have much of a problem. As someone pointed out, Westerwelle hasn't had any problems right. And Iceland already has a lesbian Prime Minister.
That being said for the sake of us gays good reputation everywhere I hope the first gay chancellor isn't a crappy Berlin communist.
Also as someone pointed out polls two years before an election does not mean anything. Otherwise Margret Thatcher would have been a one-term Prime Minister, Kevin Rudd would have won a decisive victory in the 2010 Australian election, Olof Palme would have been rejected by the Swedish voters for a fourth time in 1985, and our current PM would be named Mona Sahlin. And even if the left were to win the next German election, not too long ago the Greens were at SPD's heels for largest left-wing party. That trend might very well return.
EDIT: I'm guessing Franzl would immigrate if that happened. He hates Wowereit with a burning passion.
(It's alright, you'd always be welcome in Sweden Franz)