Once CS:GO is stable with war3source.. how hard would it be to merge it into my current branch (without changing what my branch can do) ?

Can the SVN program merge them without having to do it manually?

Yes, subversion can merge any changes from the trunk back into your branch.

Usually you would perform the merge on the root directory of your branch (/customstuff/branches/diablo) and merge in  the root directory form the trunk, but since the main directory of the trunk is the root directory, which includes your branch, you might have to do it 1 file/directory at a time