This might be kind of clunky as I am a bit of a beginner as well...
I suggest adding a second column to your CSV file (I recall the documentation saying that a csv file must have at least 2 columns anyway.). Like this
DOMAIN, FLAG
company.com,0
comp2.com,0
comp3.com,0
The value in your new, second column is the same for every row (in this example "zero")
| inputlookup whitelist_domains.csv | rename DOMAIN AS domain
| append
[search yourQueryHere | stats count BY domain]
| stats sum(count) AS Count, values(FLAG) AS Flag BY domain
| where isnull(Flag)
This will give you a list of the domain that are not in your whitelist (along with a count of events if you care)
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