This is mostly a rhetorical question, as far as I've checked the answer is 'don't even bother', but I wanted to be really sure.
We have an email app, where you can send email to lists of subscribers. This is not spam: it's used, for example, by an university to send communications to its students, by a museum to send emails to subscribers, etc.
Recently, I was asked by a prospective client if it was possible to send html messages containing javascript without being marked as spam.
Not knowing, I did a short trip of the webs and what I've got is (percentages out of my posterior) 'half the clients won't display properly', 'half the clients will flag you as spam' and 'half the clients will have blocked javascript altogether' (There's clearly some superposition).
So the best solution seems to be adding a link to a proper page if really necessary. Have you got a different experience? Do you know of any email-merge solution that provides this feature? Do you know if specific clients accept it or refuse to display html with javascript?
You have listed the right arguments against javascript usage in emails. These show you that it is a bad idea. Linking to a page where you can use javascript freely is a good option and lets the user decide if and when he wants to access this "enhanced" content.