If your worry is simply that non-empty fields will be overwritten with new data, then block field updates from forms (in Field Management) and you'll be fine.
If your worry is that *some* updated data may be valuable, while other data should be discarded, you should submit data to a proxy field instead for manual human review.
Company Name is a field on the lead/contact object. This does not affect the account name which is tied to the opportunity object. Before you go and create a bunch of parallel fields and then have to write a whole bunch of smart campaigns to populat those proxy fields, you might want to consider how often this happens and what data that is going to impact.
One additional thing to keep in mind. Unless you have specifically requested that Marketo allow your instance to make updates to the account level, typically you cannot make changes to account fields from Marketo. So, things like Company Name will not be impacted once there is an account that they're linked with.