Removing useless merge commit with "filter-branch"

Hi,

I have a large project (~100K commits) and I need to split a part of it into separate project. What I usually do in this case is

git filter-branch --prune-empty --index-filter 'git rm -rfq --cached --ignore-unmatch UNNEEDED_DIRECTORIES' HEAD

that works more or less fine for me.

The original project has a lot of merge commits (don't ask me why). Basically every non-merge commit is merged back to master branch instead of rebasing on top of the master. In the command above I use --prune-empty parameter that removes empty commits, but not their merge points. This leaves a lot of "useless commit points" like this:

|
o      - merge commit that previously merged feature X
|\
| \
|  \
o  |   - real commit
|   |
|  /
|/
|

As of me such merge left-overs are completely useless and I would like
to remove them. Actually this task can be split into 2 steps:
1) Remove useless parents. A useless part is the one that points to a
commit that is *already* reachable by some other parent. This step
converts useless merge points to regular empty commits.
2) run filter branch with --prune-empty that removes such empty commits.

So my questions are:
1) What is the best way to remove "useless parents" as in the algorithm above?
2) Should such behavior (remove useless parent/merge commits) be
enabled when flag --prune-empty is used?