My company just started using SFDC this year. We've always targeted accounts, not leads so the leads and contacts definitions have been extremely difficult to get used to. Therefore, we are transitioning everyone to accounts & contacts.
I'm concerned how this may affect the Marketo and Salesforce system. If you have any insights or know of any unintentional effects that this process may cause, I'd appreciate your sharing them with me.
In terms of how this affects your systems, it shouldn't. In fact, it might even help. Marketo considers leads/contacts in salesforce as "leads" for smart lists/segmentation. By converting all leads to contacts, you'll now be able to have standardized data from the account that would by default append to the lead. The only issue you might find is if you try to update account-level info like address, employees, or annual revenue. This company-level data would need to be updated in Salesforce or through third-party tools.
I know it's on the roadmap for Marketo ABM (Q1 2017?) to release the ability to convert leads to contacts in flow steps, however this functionality is not supported right now. My recommendation in the meantime to batch convert leads into contacts would be to review 3rd party tools like DemandTools (PC only) or Cloudingo. If you're looking for something on the automation side, I would check out Engagio or Lean Data - both predict lead to account matching based on criteria you define.
Hope this info helps.
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