There are a couple ways to go about this. If you've already connected to a DC for that domain in the past (sounds like you have), then you can disable the auto reconnect for that domain as you said. The default failed attempts value is 15 and it checks the domain for a DC every 2 minutes. So after about a half hour, Unity should stop trying to reconnect to this domain for a DC. Reboots/service restarts might affect this...you'd just have to test to find out.
The other thing you can do is if the domain is being taken offline for good, it is possible to delete that domain and associated info from the AD Domain table in SQL.
I'd say go with Option 1 first and see if it provides the results you want. If not, open a TAC case and inquire about Option 2 or possible other options.
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