Suggestion #1
You could do a little bit of LINQ manipulation after you execute the query to grab the data you want.
var result = Session.QueryOver<Entity>()
    .Where(e => e.Id == entityId)        // Filter,
    .Fetch(e => e.ReferenceEntity).Eager // join the desired data into the query,
    .List()                              // execute database query,
    .Select(e => e.ReferenceEntity)      // then grab the desired data in-memory with LINQ.
    .SingleOrDefault();
Console.WriteLine("Name = " + result.Name);
It's simple and gets the job done.
In my test, it resulted in a single query.  Here's the output:
SELECT
    this_.Id as Id0_1_, this_.Name as Name0_1_, this_.ReferenceEntity_id as Referenc3_0_1_,
    q5379349_r2_.Id as Id1_0_, q5379349_r2_.Name as Name1_0_
FROM
    [Entity] this_
    left outer join [ReferenceEntity] q5379349_r2_
        on this_.ReferenceEntity_id=q5379349_r2_.Id
WHERE this_.Id = @p0;
Suggestion #2
Another approach would be to use an EXISTS subquery, which would be slightly more complex, but would return the right result the first time without any need for post-database manipulation:
ReferenceEntity alias = null;
var result = Session.QueryOver(() => alias)
    .WithSubquery.WhereExists(QueryOver.Of<Entity>()
        .Where(e => e.Id == entityId)                 // Filtered,
        .Where(e => e.ReferenceEntity.Id == alias.Id) // correlated,
        .Select(e => e.Id))                           // and projected (EXISTS requires a projection).
    .SingleOrDefault();
Console.WriteLine("Name = " + result.Name);
Tested - results in single query:
SELECT this_.Id as Id1_0_, this_.Name as Name1_0_
FROM [ReferenceEntity] this_
WHERE exists (
    SELECT this_0_.Id as y0_
    FROM [Entity] this_0_
    WHERE this_0_.Id = @p0 and this_0_.ReferenceEntity_id = this_.Id);