There's presently (MongoDB 2.6) no way to $hint an aggregation pipeline; the request for this feature is
SERVER-7944. As mentioned in that ticket, you can use
index filters to control index selection in an aggregation pipeline if the pipeline begins with a $match.
I'd also suggest providing more details about the pipeline and the suboptimal index selection to the list and we'll see if we have any other advice for your particular problem. Please include the offending pipeline, an explain, a sample document, and the version of the C# driver.
-Will