Sure, you can do this anytime. Just put the checkbox or field in SFDC first and it will sync to Marketo.
if you prefer to only worry about syncing from Marketo > SFDC, then you can make a custom Marketo field (which won't sync to SFDC).
In your workflow for MQL, just make sure that the flow looks only for leads with the field=TRUE (ok to sync).
If you're worried about sending leads from SFDC to Marketo, then all you need to do is have the Marketo User be unable to see records with that checkbox=true.
I have heard of other firms doing this, so go ahead.