I believe it was considered rape when he stuck his fingers inside her as he held her down on his lap.
I thought she was aiming at his crotch, not his knees. My takeaway from that scene was that she shouldn't make a false, and therefore useless, threat against a perp. Everyone knew she was never going to pull the trigger.
I know there are a lot of Benson/Stabler shippers out there but the whole thing just skeeves me out. It just seems so forced. They are much better as friends.