Free e-mail account is very easy to setup than to setup an e-mail address with a company in background together with a web site. There are lots of companies refuse to do business with free e-mails. I do not suggest to completely avoid, but what I say that you must be careful with the orders done with free e-mails. Free e-mail is another positive point to your fraud scoring system.
Also, keep in mind that, marking an order for extra check for fraud, depends on your business model. If you target end-users, or let your customers try before buying, your customer may want to try or buy with a free personal e-mail. On the other side, if you explicitly sell to companies, or your products are highly priced, you must watch free e-mails.