We haven't been able to come up with a workaround for this behavior. I think the only solution is for Marketo to handle this more elegantly by automatically merging an unknown with a known lead that has the same email address. I thought that there was an Idea for this, but I couldn't find it, so I will submit one.
What we do when this happens, is send an email alert to the sales rep to alert them that an unknown Marketo lead was created potentially because they didn't wait long enough, but sometimes because they didn't create a Lead or they had a typo in the email address when they they sent the email or they responded to an existing Lead, but the lead used a different email address that the one in the Lead record. This does have some mitigating effect on their behavior and they do respond and either tell us what happened, so we can take corrective action (e.g. merge the unknown Marketo lead into the appropriate record and sometimes delete it).
In the case where they created the Lead, but didn't wait long enough, we have an email duplicates smart list and every day we merge all of the unknown lead records with their known lead record mate.