I had the same question after viewing last night's launch, specifically regarding the fact you could drag-and-drop Pardot reporting onto the main page. I'm assuming we'll be able to do the same thing with MSI (I'd love to force this on our sales team's homepage), but you never know!
Do you mean "will Marketo MSI" work with Salesforce lightening? My guess is that the team are already hard at work enabling this to be part of the new interface but tbh - the MSI is simply built with standard SFDC components which will upgrade as normal as part of their excellent upgrade process. Will Marketo work behind the scenes aka Connector/API? The answer is yes.