While doing an external merge, the entire SourceTree app is disabled until the merge tool exits. This is unfortunate; it's often necessary to examine the history of the branches involved in the merge when deciding what the result should be, but this is impossible with the current behaviour.
Ideally we would be able continue to use SourceTree during a merge. But if you really feel it's necessary to disable SourceTree, at least limit it to disabling the current tab, so we can access other repos.