I recommend you check out
Cloudingo for Salesforce to handle mass merges in SFDC. Any merging of leads you do in your CRM in an integrated setup will roll up to Marketo accordingly.
Alternatively, you could engage the Marketo Services team to do a 1-off "EasyMerge" project. If duplicates won't be an ongoing problem for you after one batch merge this option could be worth a look as they will do all the legwork for you.
Some other potentially useful info:
https://community.marketo.com/MarketoArticle?id=kA050000000LJSHCA4
https://community.marketo.com/MarketoArticle?id=kA050000000KyszCAC
https://community.marketo.com/MarketoArticle?id=kA050000000L3EnCAK