Why does Pip feel guilty for not being truthful with Joe?

A. Because he knows the truth

Joe is well aware that Pip's treatment of him is inspired by ambition rather than love. Pip wants to get ahead... to be a gentleman.... Joe brings him down. It matters not that they are family, or that they care about each other. Pip's guilt stems from his feelings for Joe. He feels guilty because he loves and respects him, but in the end, he lies because his wants and needs come before all others. His guilt doesn't stem from the way he feels, but rather, because Joe knows him well enough that he knows the true reason.