I don't have a fixed headcanon for certain things, like what happened to Spike's family. What I imagine at the time is what I go with. I usually go with the idea that his mother is dead, but sometimes other scenarios such as this one pop into my head.
In this particular scene Spike is at his mother's cave and she is wonderful to him. He's torn however, because on the one hand he has a loving mother who would suffer if he left, yet on the other hand he cannot stop thinking about Ponyville and especially Twilight.
I think a scene like this would work much better if the dragoness was actually not his real mother, but in fact just a very caring female who's obviously not his mother. This would be much less complicated and controversial and it would require a lot less explanation. Spike could still have the same feelings about parting with her, since he never really had a consistent mother figure in his life and now that he does, he knows what he's been missing out on.