Hi Vlada,
The problem you're having is the there are 2 separate records in Marketo that have the same email address. So it you add record 1 with email address John 1 12345@1234.com to Email 1, and then do "not was sent email" or something to exclude him from Email 2, it can still pick up the second record John 2 since Marketo doesn't see it as a dupe.
If you feel like going super manual after you send email 1, you could copy all the email addresses that were sent the email and create a smartlist using the email address as the screening factor.
But the hideous nightmare of doing that over and over manually pretty much defeats the whole "automation" piece.
ReachForce (my company, watch out, here comes the shameless plug) does free email quality assessments so you can at least get a sense of your duplication level and other email quality issues, and a lot of Marketo users take advantage cause, this is a problem for a lot of us.