You can use a change data value, but only if the records you want to update are Marketo only or leads in the CRM. If the records are contacts, the company values will apparently update but revert to original value on next sync. In that case, you will have to do the update in the CRM.
My advice: create a smart list to identify the leads using company name and email domain. You will probably need to tweak the criteria a few times as you'll find companies that use multiple email domains and company names that are spelled differently.
Export that list, make a copy of the file, then make your changes in Excel. When you're satisfied, import it back into Marketo.
Unless you have a DEV instance that's in sync, you REALLY don't want to change data in Marketo unless you're 100% confident (hint: you should never feel 100% confident.). Having a backup is great so you can revert if you mess things up.
My suggestion is to test it on a few leads in Marketo (add a filter to include about five-ten leads) to see if your updates applied in Marketo are correctly transferred to CRM. If everything works correctly on these few leads, then you can apply it to your whole batch of leads