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Reading through the 'at' source code it is a fairly trivial patch to alter the mail header that the at command creates to include a content-type field. The complete answer may be to add an environment variable e.g. AT_CONTENT_TYPE or a command line argument e.g. -c that the at command checks and validates the value against two allowable values being "plain" ...
Send the message explicitly from your script, rather than just print the output and rely on at to send the message. Write the HTML to a file and use mutt to attach it and send the message. Alternatively, write the message with headers, MIME structure and all, and pipe it to sendmail -t -i. Using mutt is the easier way by far.
I don't think it's possible to natively do what you are looking for. I'm not aware of any at implementation having the ability to, from within the job, make any real changes to the resultant message headers. However, you could run the script as a sub-process that produces HTML output, redirect that output into a file, and add any surrounding headers as ...
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