I am playing on version 0.9.1b and I noticed that choosing to skip the prologue while in hard mode has the loan cleared, even though it wouldn't be clear if you played the prologue normally. Additionally,  in all modes, you also lose out on items you'd normally get when siding with a guild. I don't think the items are super important, however, compared to hard mode basically requiring you to play through the prologue if you want to play it as intended.