Consider just ignoring the lack of smallcaps in ADE. There could be a new version of ADE launched tomorrow with support for smallcaps, or readers could start adding support for them independently, or ADE may be discontinued and a new ePUB reader take its place.
Nevertheless, the idea of using a smallcaps font is good. Since it's a workaround for ADE, you could wrap it in this conditional CSS
. You could also use bold or underline instead of smallcaps in ADE.