I would need to know some more of the context to be absolutely certain, but I'm pretty sure that you are correct. There are two different occasions when one might have one's fingers crossed.
1. You are not telling the truth [as in this case]. The idea is that having one's fingers crossed while you do it absolves you from the sin of untruth.
2. You are hoping very much for a successful outcome. For example: "I'm keeping my fingers crossed that I win the Lottery this week".