Budget Hostels in Istanbul
Since startups stay longer (between 27-30th September), hostels can be a good solution for lower costs.
You may find budget hostels here or here by this link.
As you already know, the training will be in Microsoft Building shown below and the event will be in Lutfi Kirdar Convention Center shown in a previous post.
It is better to find a hotel/hostel close to Taksim/Beyoglu to be in a good location for all the event and also attractions of Istanbul.