He couldn’t keep flipping and flopping back and forth. He simply had to make a decision. The Doctor had been putting off seeing and spending time with Aria for a long while. He hadn’t even started thinking about that wedding he promised her.
To put it more accurately, he was running away. The Doctor was running far away from Aria, Geronimo, his problems, everything, Now he was sitting in his TARDIS alone having thrown out his other selves as well, even threatening them a little to keep his secret. He needed time to think, to sort out his confusion and right this mess.