Marketo will allow you to send the same email to a lead twice. Hoever, in the scenario you laid out, you won't have a problem.
If you send the emails using one smart campaign that has the criteria Lead is in SFDC campaign X or Y, you will only be pulling one lead into your smart campaign even if it is in both SFDC campaigns. You could run into some problems if you're trying to change the SFDC campaign status based off of activity with the email, but you won't send two emails.
NOTE: If you use separate smart campaigns to pull in the leads from the two campaigns (one smart campaign for each SFDC campaign) then you would end up sending to the same person twice.