You could always do this:
1. Create a dummy text field in Marketo only... something like "Email Holding".
2. In your flow, use Change Data Value three times, like so...
3. Change Data Value: "Email Holding" to {{lead.email address}}
4. Change Data Value: "Email Address" to {{lead.alternate email address}}
(might want a short wait step to let the system catch up)
4. Send email
5. Change Data Value: "Email Address" to {{lead.email holding}}