Here's Bernie's response to my question on mongodb-user:

We don't currently support this but it's a cool idea. You could open a
jira case to request an enhancement for a $comment operator.

I haven't tested this but it might work to add a parameter to your
query that never exists. Something like:
find({<your params>, fakeComment:{$ne:"some comment"}})

Unfortunately that will likely have the side effect of slowing the
queries down even more.