Unique insert performance: Primary Key vs Unique Index
From your question, I'm not completely sure if you're inserting multiple values per query, but you definitely should be.  With MyISAM as the engine, there should not be a performance difference between the index being UNIQUE or PRIMARY; MyISAM doesn't treat them differently in this case.  If you were using InnoDB, however, there would be a difference since it stores the data in primary key order.  If you don't need the id column, removing it and making domain the primary key would help performance.

Changing the collation should help since ascii is much simpler than utf8, but you might want to use ascii_general_ci instead of ascii_bin since domain names are case-insensitive.

One other way to do the queries would be to get the number of rows, INSERT DELAYED, flush the delayed writes, and then get the new row count.  The difference in the counts would be the same as the affected rows.  However, I don't think this would be significantly faster, but it would make the process more complex.