I'm not aware that there was a debate, if Obama should be allowed to speak at the Brandenburg gate.

After complaints by the current US administration our chancellor office announced 'only limited understanding' and 'skepticism about pursuing such plans', but has made perfectly clear, that a decision is not to make on the federal level. No word about forbidding anything.
So if Obama would have insisted on using the Brandenburg gate, he most likely could have done so. It was his decision to use another place.

Furthermore I think Merkel's protest was only for the reason, that Americans don't perceive Germany as partisan in the US election. I have doubts, that Merkel really has a problem with Obama speaking at the Brandenburg gate. Speaking there is nothing you have to earn in Germany (see Westerwelle's 'Piesepampel' comment), but in the US. And being elected president qualifies for that.

And with the visitors, I think there will be the 100,000+ visitors.

Der Amerikaner ist die Orchidee unter den Menschen
Volker Pispers