If it is called rape or not and on which occasion is mainly decided by whose POV is made to be most important. Especially in the first season, we are mostly inside the Dollhouse, sharing the very skewed view of the various handlers, of Topher and DeWitt, all of them reliably sociopathic considering they even work for this institution in the positions they are in. Ballard might see it differently at the beginning, but it is this character's most notable failing that in season 2 he is far too accepting of the ways things are done (and people are treated) in the Dollhouse.
Aside from that, the show does ravel in the rapefantasies rather than distance itself from the Dollhouse's general wrongness - and that really is its biggest problem: you cannot have the interesting story without getting lots and lots of bullshit thrown at you.