I believe you want that the Smart campaign should be triggered for all the leads which are from your list of 1000 companies. Also, at the same time, you do not want to create a category object in SFDC.
You can get the list of your 1000 companies in Marketo filter.
You can create a filter for all the leads which are created after today's date and another filter for company name. The filer of company name would have comma separated values for all 1000 companies.
After this, when you schedule the campaign, it will be triggered only for the new leads from these 1000 companies.
I hope this works for you.