Did you try adding something like this to the css (from the link I gave above)?
Code:
.olde {
-moz-font-feature-settings: "hist=1, liga=1, dlig=1";
-ms-font-feature-settings: "hist", "liga", "dlig";
-webkit-font-feature-settings: "hist", "liga", "dlig";
-o-font-feature-settings: "hist", "liga", "dlig";
font-feature-settings: "hist", "liga", "dlig";
}
The order of "hist", "liga", "dlig" may be important (it was for Prince), so try different permutations. All these properties may be overkill anyway, "font-feature-settings" would be the one to choose for the future, and iBooks could use "-webkit-font-feature-settings", the others are unlikely to be used by any reader.
I wouldn't be surprised if ADE (and derivates) did not offer any way to access these OpenType features. But, as I said, the text would still be readable, searchable and have an old look... and would be automatically upgraded whenever Adobe decides to write a decent reader.
In any case, if I'm right with my assumption above that writing an explicit long-s in your input would unleash all its ligatures with no further action on your part, that's not an entirely bad option.