Unless, they are made of Stainless Steel or silicone, I wouldn't because pouring soap into any mold can be messy, and any spills with active lye still in it (CP soap batter) will react with the metal.
Also, as others mentioned, the cupcake paper is not coated like Freezer paper and the soap batter will be absorbed and surely contaminate your muffin tins, causing a reaction with the metal.
Re: your concern about the paper sticking to the soap: I have used parchment paper (which I think the cupcake papers are made of, but not sure) and it usually comes off okay, but if you use a colored or patterned parchment paper, the colors and the pattern become embedded onto the surface of the soap. That happened to me when I used parchment paper with a colored pattern design. It looked sort of dirty, not pretty at all.