I'll have to check to make sure, but I suspect disabling associations is harder than that, as associations for programs internal to Wine (eg. notepad) get created during the initial wineprefix creation or (at the latest) the first time any application (even winecfg) is run, meaning it would be too late to uncheck a checkbox in winecfg afterwards. Instead, it might be possible to ask the user the same way we ask for Gecko and Mono - that hopefully happens early enough.
I would much prefer that we have sane defaults, i.e. don't export Wine's default associations for file formats that aren't Windows-specific (.txt files). For Windows-specific formats, it's probably better to put those in wine.desktop as well, which simplifies the rule.