I just downloaded the updated 2.1 version of BG:EE and after copying the App to my Application Folder and starting it the following error is shown: ‘"Baldur's Gate Enhanced Edition" is damaged and can't be opened. You should move it to the Trash.'
I downloaded the file twice, md5 checksum is 3fb656c4ec6b6de918e31bb997d8756e
After unpacking the App's info dialog show 3,04GB usage on disk and version 2.2.0.12 (2.1.63.2)
Any ideas how to fix this?

Are you talking about the mac version? I have the same problem. Download seems ok as I already downloaded the image from the webpage again. The disk image (dmg) opens without any problem, but after starting the app the self-check stops and MacOS recommends to remove the damaged app. Btw, I'm using Mac Os 10.11.4.

Edit: Thanks to Time Machine I restored version 2.1, which runs without any problem.

Edit2: I need to correct myself. The old and restored version is 2.0.6.2.2. I used the version number MacOS showed me first in the column (2.1.0.11), but the correct one seems that one in the bracket behind.

I took another attempt and downloaded the installer again. No luck with that, as the problem still exists, but then I wanted to know if the game is in general broken or if it's just the installer. I installed GOGs client Galaxy and installed the game. Using the client it runs without any problem, which means only the installer is broken.

Edit: I downloaded the installer via Galaxy and checked the md5-checksum, it's the same file as from downloading using the browser. So it's clear, the version inside the installer is broken and gog needs to upload a working one. In the meantime the only option to play the game is to install the game using Galaxy.

You should send in a support ticket if you haven't already.

I did and got an answer from them. They are aware of the problem and looking into it. They also wrote me a short workaround how to make the game runable without the need of Galaxy.

You can use this workaround:
1) Open the Terminal
2) Type in:
xattr -r -d com.apple.quarantine
make sure that there is a space at the end, don't press Enter.
3) Drag the application to the Terminal window, this should add the correct path.
4) Press Enter