The process I've followed is "disabling" SFDC campaigns by unchecking the "active" box. That will hide the campaign from being findable in Marketo, but it shouldn't remove the link between an existing Marketo program. It will also hide the campaign from picklists for SFDC users to choose from when tagging campaign codes, so it's handy for keeping your campaign list manageable. It doesn't delete any data, you can still report on the campaigns, and if it needs to go active again, you simply toggle the active checkbox to true again.