As Adam says, one option would be to use SMTP Relay...
https://help.exacttarget.com/en/documentation/exacttarget/interactions/triggered_emails/sending_exacttarget_emails_via_smtp_relay/
On the CRM side of things, you can configure SMTP relay...
https://help.salesforce.com/HTViewSolution?id=000005793&language=en_US
This would route all workflow emails via SFMC from what I read. You'd have to discuss how to send selectively via SFMC with some Salesforce CRM experts (of which I'm definitely not one).
Taking another tack, I can only take you so far with Marketing Cloud. You can trigger an SFMC email either by rolling your own Apex triggers in CRM, or using the relatively new Triggered Send functionality of the V5 connector (the object needs to a have lookup field related to a CRM Lead or Contact)...
https://help.exacttarget.com/en/documentation/integrated_products__crm_and_web_analytic_solutions/marketing_cloud_connector_v5/sending_emails/triggered_sends/
If the object's not directly related the the Lead or Contact, you'll need to roll your own trigger or the likes to access SFMC's APIs directly.
You can use the AttachFile() AMPScript function within the SFMC email to pull in an attachment from a URL and this URL would need to be passed in as a personalisation string or you could do some Salesforce AMPScript in the email to go search for this value, somehow.
Your challenge would be to make the attachment publicly available so that the AttachFile() can access the file. Using sites in Force.com, here's an example of a thread talking about how to do this...
https://developer.salesforce.com/forums?id=906F000000099hpIAA