The simplest solution (ignoring the rights and wrongs of the whole issue) would be for commercial users to reclaim the duty paid. (There are already other instances where registered users of other items can reclaim duties) - and which are not known to the general public). The whole thing is managed via the VAT regime.
This ensures that MGO would still exist as a product and would distinguish between non road fuel and road fuel use. That way would mean that a different rate of duty could be applied to "leisure users" - hopefully at the EU minimum rate (.30 Euro per litre) which might be adjudged as acceptable to most boaters?
Don't forget that there are many other users - some small - of MGO who are not leisure users (e.g builders, domestic heating, "tractors" and so on) and for which MGO would have to be available in one form or another.
This whole suggestion is so simple, that (always cynical) I doubt that it would be taken up....