Okay then, in that case what you need is the *--squash* option of 

--squash, --no-squash 
> Produce the working tree and index state as if a real merge happened 
> (except for the merge information), but do not actually make a commit, move 
> the HEAD, or record $GIT_DIR/MERGE_HEAD (to cause the next git commitcommand 
> to create a merge commit). This allows you to create a single 
> commit on top of the current branch whose effect is the same as merging 
> another branch (or more in case of an octopus).
> With --no-squash perform the merge and commit the result. This option can 
> be used to override --squash. 

In your case, you'd probably want to use it like so:

$ git checkout DST
> $ git merge --squash SRC

Basically, it'll produce a diff between SRC and DST and add it to the index 
without committing or merging the histories.

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