Can I block the techtree advancing from the medieval era somehow?
That would require some light modding.
Each technology in the file CIV4TechInfos.xml has a value called bDisable and it is valued 0. I wouldn't be surprised if valuing it 1 would actually disable that technology. But I must admit that I haven't tried that before. Ask around in the Creation & Customization forum for expert advice on modding.
I have a great scientist, in the long run is it better to have him as a great scientist, +2500 for education or build his special academy?
If there were a universal answer to this question, then why would there be 3 uses for this Great Person (4 with the Golden Age option).
Sometimes, you can really really use a technology and it will be great for trading purposes or being the first to that technology will give you a nice special bonus (like for instance the free technology for Liberalism).
The Academy increases the base science output of a city by 50%. That can be quite a lot in a good science city. If a city on average (at your typical science percentage) has a base science output of 60 (before bonuses of libraries and universities), then the Academy adds 50% of 60 is 30 science per turn. After 100 turns, that amounts to 3000 science. But of course, 100 turns is quite a lot of waiting time.
A great scientist specialist adds 1 hammer and 6 science per turn. Both are multiplied by various bonuses from buildings. For instance, with the bonuses from a forge, factory and power plant, the 1 hammer becomes 2 hammers. With the bonuses from a library, a university, an observatory, a laboratory, an academy and Oxford University, the 6 science becomes 6 + 250% of 6 is 21 science.
At the start of the game an Academy won't add that much as there are no cities with a great science output. But of course, it will add science during the length of the game, so the bonus will increase if you add an Academy to a city with a great potential science output. The bonus from the great scientist will also increase once building modifiers multiply the bonuses. Some of the power of lightbulbing a technology is lost at the start of the game because the technologies are so cheap at that point. The starting technologies cost a lot less than 2500 science.
All that being said, I probably use the great scientist most for building an academy and for (one of the contributors to) a golden age.