For anyone struggling here, this gist solve the issued for me. It does: 

sudo ln -s /usr/local/bin/git-crypt /Applications/SourceTree.app/Contents/Resources/bin/

I started having an error stating that git-crypt command was not found and I applied Ben Gestug's command solution with current version and now it's working again.

sudo ln -s /usr/local/Cellar/git-crypt/0.6.0/bin/git-crypt /Applications/SourceTree.app/Contents/Resources/git_local/bin/git-crypt

I started suddenly receiving error messages that git-crypt smudge failed.

I can also confirm that running Ben Getsug's command worked as a solution. But updated with current version of git-crypt of course.

sudo ln -s /usr/local/Cellar/git-crypt/0.6.0/bin/git-crypt /Applications/SourceTree.app/Contents/Resources/git_local/bin/git-crypt

I can also confirm that Ben Getsug's solution worked for me.

MacOS 10.13.6 (17G65) with Sourcetree 2.7.6 (177).

Solution provided by Ben Getsug worked for me. Thanks Ben.

If you want to use embedded git with external git-crypt (installed with Homebrew), creating the following symlink seems to work:

sudo ln -s /usr/local/Cellar/git-crypt/0.5.0/bin/git-crypt /Applications/SourceTree.app/Contents/Resources/git_local/bin/git-crypt

Confirmed working with system git on latest Mac OS X 10.11.5:

# which git
/usr/bin/git
# git --version
git version 2.7.4 (Apple Git-66)
# which git-crypt
/usr/local/bin/git-crypt  # installed from Homebrew

This should work if you choose to use the system version of git instead of embedded and ensure that git-crypt is a part of the PATH it sees. The easiest solution would be to symlink git-crypt to the same location as your git binary due to variations in how to configure (per major OS revision.)

+1 I wish git-crypt was just built in to git, but alas. It would be nice to support it at least on a basic level, versus getting 4 of these in a row anytime ST detects a change.

does a workaround exist to resolve this issue?